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From: Pablo C. <pc...@cn...> - 2020-10-05 10:15:51
|
Hi Wolfgang ... we have recently added a new feature that is releated to
the queue parameters.
With the latest version you can edit the parameters before
"executing/scheduling" the protocol.
If they are populated (copying a protocol will keep the parameters) the
user is not asked.
We were currenlty discussing this, and Jose Miguel already suggested to
ask, at least once to verify de queue parameters and we will do so.
Maybe, with current code (3.0.4), you can remove the queue parameters in
the template, so users will be asked. (I'm guessing you have queueParams
poplated in your template)
Does it make sense?
On 5/10/20 11:29, Lugmayr, Wolfgang wrote:
> hi,
>
> we have 2 queues on our cluster, one for cpu jobs and one for gpu jobs.
> so far my template was working fine, but since 3.0.3 and now 3.0.4 scipion always takes the last entry in the QUEUES section of the hosts.conf file.
>
> before a window pop-up appeared after pressing the Execute button and users could choose which queue and which parameters they want to have.
> this defines the nodes the users will get.
>
> now the pop-up window is gone and the job script is generated with the settings of the last queue entry.
> in this case maxwell-gpu.
>
> QUEUES = {
> "maxwell-cpu": [
> ["JOB_QUEUE","cssb,all","Queue Name:","Select the target queue/partition"],
> ["JOB_TIME", "168", "Time (hours)", "Select the time expected (in hours) for this job"],
> ["JOB_NODES","48","Total cores:","MPI tasks"],
> ["JOB_CONS","Gold-6126","Constraints:","Call sinfo_detailed on the commandline for the options"]
> ],
> "maxwell-gpu": [
> ["JOB_QUEUE","cssbgpu,allgpu","Queue Name:","Select the target queue/partition"],
> ["JOB_TIME", "168", "Time (hours)", "Select the time expected (in hours) for this job"],
> ["JOB_NODES","1","Total cores:","1: Single program call with threads and no MPI"],
> ["JOB_CONS","GPUx1","Constraints:","Call sinfo_detailed on the commandline for the options"]
> ]
> }
>
> is there a new way to do this, so i have to update my template?
>
> cheers,
> wolfgang
>
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Lugmayr, W. <w.l...@uk...> - 2020-10-05 09:29:36
|
hi,
we have 2 queues on our cluster, one for cpu jobs and one for gpu jobs.
so far my template was working fine, but since 3.0.3 and now 3.0.4 scipion always takes the last entry in the QUEUES section of the hosts.conf file.
before a window pop-up appeared after pressing the Execute button and users could choose which queue and which parameters they want to have.
this defines the nodes the users will get.
now the pop-up window is gone and the job script is generated with the settings of the last queue entry.
in this case maxwell-gpu.
QUEUES = {
"maxwell-cpu": [
["JOB_QUEUE","cssb,all","Queue Name:","Select the target queue/partition"],
["JOB_TIME", "168", "Time (hours)", "Select the time expected (in hours) for this job"],
["JOB_NODES","48","Total cores:","MPI tasks"],
["JOB_CONS","Gold-6126","Constraints:","Call sinfo_detailed on the commandline for the options"]
],
"maxwell-gpu": [
["JOB_QUEUE","cssbgpu,allgpu","Queue Name:","Select the target queue/partition"],
["JOB_TIME", "168", "Time (hours)", "Select the time expected (in hours) for this job"],
["JOB_NODES","1","Total cores:","1: Single program call with threads and no MPI"],
["JOB_CONS","GPUx1","Constraints:","Call sinfo_detailed on the commandline for the options"]
]
}
is there a new way to do this, so i have to update my template?
cheers,
wolfgang
--
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Deutsches Elektronen-Synchrotron (DESY)
Notkestrasse 85 Gebäude 15
22607 Hamburg, Germany
Tel.: +49 40 8998-87652
Email: wol...@cs...
http://www.cssb-hamburg.de/
|
|
From: Pablo C. <pc...@cn...> - 2020-10-05 08:09:15
|
This is just a guess. hdf5 files might be provided by the system (yum/apt-get install hdf5-dev) But actual hdf5 libraries....are taken from conda? What if they do differ? Is this what is happening? David Maluenda, others, could this be the case? On 5/10/20 9:35, Jorge wrote: > > Hello Tao, > > We've been updating the documentation these days. The following link > contains detailed information and instructions about how to install > Scipion3 in different Linux distributions, and may solve your hdf5 issue. > > https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html > > Please have a look and in case the problem remains, do not hesitate to > contact us. We'll be pleased to help you. > > Have a good day! > > Jorge > > > On 10/3/20 8:48 PM, 王涛 wrote: >> hello everyone, >> I got a problem while installing scipion3 with miniconda. >> I installed conda at first,then: >> >> pip install --user scipion-installer python3 -m scipioninstaller >> /path/where/you/want/scipion -j 4 >> then program failed in compiling module 'xmipp',and log showed that there may be some errors in linking >> hdf5 library,but I have hdf5 installed by conda with default channel. There is another warning about >> libjpeg.so at /usr/lib64 in error logs, so I think program may not find library in .scipion3env as normal,and >> I don't know which file should I configure.(maybe xmipp.conf or SConscript or SConstruct?) >> (.scipion3env) [raozh@mgmt01 scipion3]$ conda list hdf5 >> # packages in environment at /home/raozh/wtao/conda/miniconda/envs/.scipion3env: >> # >> # Name Version Build Channel >> hdf5 1.10.7 hb1b8bf9_0 >> Anybody got any idea about this? >> Thanks for any help. >> Tao Wang >> Ph.D candidate, >> Tsinghua University >> here are logs: >> (.scipion3env) [raozh@mgmt01 scipion3]$ python3 -m scipioninstaller /home/raozh/wtao/scipion3/ -j 4 >> conda detected. Favouring it. If you want a virtualenv installation cancel installation and pass --venv . >> WARNING: A conda environment already exists at '/home/raozh/wtao/conda/miniconda/envs/.scipion3env' >> Remove existing environment (y/[n])? >> >> >> CondaSystemExit: Exiting. >> >> Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) >> Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (3.2.2) >> Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.0.0) >> Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (7.1.2) >> Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.7.0) >> Requirement already satisfied: requests<=2.23.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (2.23.0) >> Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.18.4) >> Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.2.0) >> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) >> Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) >> Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.2.0) >> Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) >> Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4) >> Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20) >> Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10) >> Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.10) >> Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) >> Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) >> Requirement already satisfied: scipion-app in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) >> Requirement already satisfied: scipion-em in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (3.0.3) >> Requirement already satisfied: outdated==0.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (0.2.0) >> Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (3.0.4) >> Requirement already satisfied: biopython==1.76 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (1.76) >> Requirement already satisfied: littleutils in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (0.2.2) >> Requirement already satisfied: requests in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (2.23.0) >> Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.0.0) >> Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) >> Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) >> Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) >> Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.2.2) >> Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) >> Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10) >> Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (1.25.10) >> Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20) >> Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4) >> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7) >> Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1) >> Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0) >> Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) >> Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2) >> Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0) >> Scipion v3.0.4 () devel >> >> >>> WARNING: Image library not found! >> > Please install Xmipp to get full functionality. >> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) >> >> >> Building scipion-em-xmipp ... >> /home/raozh/wtao/conda/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7rc1 >> Requirement already satisfied: scipion-em-xmipp==20.7rc1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (20.7rc1) >> Requirement already satisfied: scons in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (4.0.1) >> Requirement already satisfied: plotter in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (1.3.17) >> Requirement already satisfied: joblib in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.17.0) >> Requirement already satisfied: scikit-learn==0.22.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.22.1) >> Requirement already satisfied: peppercorn in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.6) >> Requirement already satisfied: setuptools in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scons->scipion-em-xmipp==20.7rc1) (49.6.0.post20200925) >> Requirement already satisfied: numpy>=1.11.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.18.4) >> Requirement already satisfied: scipy>=0.17.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.5.2) >> Done (0.78 seconds) >> Building xmippSrc-3.20.07rc ... >> Skipping command: wget -nv -c -O /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07rc.tgz >> mv -v /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz >> All targets exist. >> Skipping command: tar -xf xmippSrc-v3.20.07rc.tgz >> All targets exist. >> cd /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc >> cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null >> Configuring ----------------------------------------- >> gcc detected >> g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include >> OpenCV not found >> rm -v xmipp_test_opencv* >> >> 'mpirun' and 'mpiexec' not found in the PATH >> Using '/usr/lib64/openmpi/bin'. >> >> 'mpicc' not found in the PATH >> Using '/usr/lib64/openmpi/bin'. >> >> 'mpicxx' not found in the PATH >> Using '/usr/lib64/openmpi/bin'. >> Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64 >> >> 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN) >> Using '/usr/local/cuda/bin'. >> CUDA-10.1.168 detected. >> CUDA-8.0 is recommended. >> Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'. >> Configuration completed..... >> Checking configuration ------------------------------ >> Checking compiler configuration ... >> g++ 4.8.5 detected >> g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_main.cpp -o xmipp_test_main.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include/python3.8 -I/home/raozh/wtao/c >> onda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/numpy/core/include g++ -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread >> /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 >> rm xmipp_test_main* >> Checking MPI configuration ... >> /usr/lib64/openmpi/bin/mpicxx -c -w -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -mtune=native -march=native -std=c++11 -O3 xmipp_mpi_test_main.cpp -o xmipp_mpi_test_main.o >> /usr/lib64/openmpi/bin/mpicxx -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_mpi_test_main.o -o xmipp_mpi_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread >> /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 >> rm xmipp_mpi_test_main* >> /usr/lib64/openmpi/bin/mpirun -np 2 echo ' > This sentence should be printed 2 times if mpi runs fine.' >> > This sentence should be printed 2 times if mpi runs fine. >> > This sentence should be printed 2 times if mpi runs fine. >> Checking Java configuration... >> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/bin/javac Xmipp.java >> rm Xmipp.java Xmipp.class >> g++ -c -w -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include/linux -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_jni_test.cpp -o xmipp_jn >> i_test.o rm xmipp_jni_test* >> Checking CUDA configuration ... >> /usr/local/cuda-10.1/bin/nvcc -c -w --x cu -D_FORCE_INLINES -Xcompiler -fPIC -ccbin g++ -std=c++11 --expt-extended-lambda -gencode=arch=compute_30,code=compute_30 -gencode=arch=compute_35,code=compute_35 -gencode=arch=compute_50,code=compute_50 -gencod >> e=arch=compute_60,code=compute_60 -gencode=arch=compute_61,code=compute_61 -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_cuda_test.cpp -o xmipp_cuda_test.o /usr/local/cuda-10.1/bin/nvcc -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt >> g++ -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt >> rm xmipp_cuda_test* >> Setting VERIFIED=True >> Building Dependencies ------------------------------------- >> make all >> mkdir -p build/ >> nvcc --cudart static -shared -link -Wno-deprecated-gpu-targets -o build/libcuFFTAdvisor.so obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTran >> sform.o obj/sizeOptimizer.o obj/main.omkdir -p build/ >> nvcc -o build/cuFFTAdvisor obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTransform.o obj/sizeOptimizer.o obj/main.o -lcufft -Wno-deprecated-g >> pu-targets cp src/cuFFTAdvisor/build/libcuFFTAdvisor.so src/xmipp/lib/ >> Compiling ------------------------------------------- >> scons -j4 >> scons: Reading SConscript files ... >> scons: done reading SConscript files. >> scons: Building targets ... >> scons: `lib/libXmippCore.so' is up to date. >> scons: `lib/xmippCore.so' is up to date. >> scons: done building targets. >> scons -j4 >> scons: Reading SConscript files ... >> scons: done reading SConscript files. >> scons: Building targets ... >> scons: `lib/libXmipp.so' is up to date. >> scons: `lib/_swig_frm.so' is up to date. >> scons: `lib/libXmippCuda.a' is up to date. >> scons: `lib/libXmippInterfaceCuda.so' is up to date. >> scons: `lib/libXmippParallelCuda.so' is up to date. >> scons: `lib/libXmippParallel.so' is up to date. >> g++ -o bin/xmipp_volume_from_pdb applications/programs/volume_from_pdb/volume_from_pdb_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhd >> f5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_idr_xray_tomo applications/programs/idr_xray_tomo/idr_xray_tomo_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhdf5 -lh >> df5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_image_separate_objects applications/programs/image_separate_objects/image_separate_objects_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion >> 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_pdb_reduce_pseudoatoms applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion >> 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore/usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 >> lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' >> lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' >> /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' >> collect2: error: ld returned 1 exit status >> scons: *** [bin/xmipp_volume_from_pdb] Error 1 >> /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 >> lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' >> lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' >> /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' >> collect2: error: ld returned 1 exit status >> scons: *** [bin/xmipp_idr_xray_tomo] Error 1 >> /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 >> lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' >> lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' >> /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' >> collect2: error: ld returned 1 exit status >> scons: *** [bin/xmipp_image_separate_objects] Error 1 >> /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 >> lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' >> lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' >> /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' >> collect2: error: ld returned 1 exit status >> scons: *** [bin/xmipp_pdb_reduce_pseudoatoms] Error 1 >> scons: building terminated because of errors. >> >> Some error occurred during the compilation of 'xmipp' ('bin/xmipp_pdb_reduce_pseudoatoms'). >> >> Traceback (most recent call last): >> File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 449, in <module> >> main() >> File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 292, in main >> installPluginMethods() >> File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods >> plugin.installBin({'args': ['-j', numberProcessor]}) >> File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin >> environment.execute() >> File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute >> self._executeTargets(targetList) >> File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets >> tgt.execute() >> File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute >> command.execute() >> File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute >> assert glob(t), ("target '%s' not built (after " >> AssertionError: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scip >> ion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')Error at main: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipi >> on3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') >> Something went wrong running: >> eval "$(/home/raozh/wtao/conda/miniconda/condabin/conda shell.bash hook)" && >> conda create -n .scipion3env python=3 && >> conda activate .scipion3env && >> cd /home/raozh/wtao/scipion3 && >> mkdir -p software/lib && >> mkdir -p software/bindings && >> mkdir -p software/em && >> export SCIPION_HOME=/home/raozh/wtao/scipion3 && >> pip install scipion-pyworkflow && >> pip install scipion-app && >> python -m scipion installp -p scipion-em-xmipp -j 4 >> Installation cancelled. >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Jorge <jji...@cn...> - 2020-10-05 07:35:29
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Hello Tao, We've been updating the documentation these days. The following link contains detailed information and instructions about how to install Scipion3 in different Linux distributions, and may solve your hdf5 issue. https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html Please have a look and in case the problem remains, do not hesitate to contact us. We'll be pleased to help you. Have a good day! Jorge On 10/3/20 8:48 PM, 王涛 wrote: > hello everyone, > I got a problem while installing scipion3 with miniconda. > I installed conda at first,then: > > pip install --user scipion-installer python3 -m scipioninstaller > /path/where/you/want/scipion -j 4 > then program failed in compiling module 'xmipp',and log showed that there may be some errors in linking > hdf5 library,but I have hdf5 installed by conda with default channel. There is another warning about > libjpeg.so at /usr/lib64 in error logs, so I think program may not find library in .scipion3env as normal,and > I don't know which file should I configure.(maybe xmipp.conf or SConscript or SConstruct?) > (.scipion3env) [raozh@mgmt01 scipion3]$ conda list hdf5 > # packages in environment at /home/raozh/wtao/conda/miniconda/envs/.scipion3env: > # > # Name Version Build Channel > hdf5 1.10.7 hb1b8bf9_0 > Anybody got any idea about this? > Thanks for any help. > Tao Wang > Ph.D candidate, > Tsinghua University > here are logs: > (.scipion3env) [raozh@mgmt01 scipion3]$ python3 -m scipioninstaller /home/raozh/wtao/scipion3/ -j 4 > conda detected. Favouring it. If you want a virtualenv installation cancel installation and pass --venv . > WARNING: A conda environment already exists at '/home/raozh/wtao/conda/miniconda/envs/.scipion3env' > Remove existing environment (y/[n])? > > > CondaSystemExit: Exiting. > > Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) > Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (3.2.2) > Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.0.0) > Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (7.1.2) > Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.7.0) > Requirement already satisfied: requests<=2.23.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (2.23.0) > Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.18.4) > Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.2.0) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) > Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) > Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.2.0) > Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) > Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4) > Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20) > Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10) > Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.10) > Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) > Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) > Requirement already satisfied: scipion-app in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) > Requirement already satisfied: scipion-em in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (3.0.3) > Requirement already satisfied: outdated==0.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (0.2.0) > Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (3.0.4) > Requirement already satisfied: biopython==1.76 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (1.76) > Requirement already satisfied: littleutils in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (0.2.2) > Requirement already satisfied: requests in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (2.23.0) > Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.0.0) > Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) > Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) > Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) > Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.2.2) > Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) > Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10) > Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (1.25.10) > Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20) > Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7) > Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1) > Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0) > Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) > Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2) > Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0) > Scipion v3.0.4 () devel > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) > > > Building scipion-em-xmipp ... > /home/raozh/wtao/conda/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7rc1 > Requirement already satisfied: scipion-em-xmipp==20.7rc1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (20.7rc1) > Requirement already satisfied: scons in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (4.0.1) > Requirement already satisfied: plotter in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (1.3.17) > Requirement already satisfied: joblib in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.17.0) > Requirement already satisfied: scikit-learn==0.22.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.22.1) > Requirement already satisfied: peppercorn in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.6) > Requirement already satisfied: setuptools in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scons->scipion-em-xmipp==20.7rc1) (49.6.0.post20200925) > Requirement already satisfied: numpy>=1.11.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.18.4) > Requirement already satisfied: scipy>=0.17.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.5.2) > Done (0.78 seconds) > Building xmippSrc-3.20.07rc ... > Skipping command: wget -nv -c -O /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07rc.tgz > mv -v /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.20.07rc.tgz > All targets exist. > cd /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc > cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null > Configuring ----------------------------------------- > gcc detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include > OpenCV not found > rm -v xmipp_test_opencv* > > 'mpirun' and 'mpiexec' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > > 'mpicc' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > > 'mpicxx' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64 > > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN) > Using '/usr/local/cuda/bin'. > CUDA-10.1.168 detected. > CUDA-8.0 is recommended. > Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'. > Configuration completed..... > Checking configuration ------------------------------ > Checking compiler configuration ... > g++ 4.8.5 detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_main.cpp -o xmipp_test_main.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include/python3.8 -I/home/raozh/wtao/c > onda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/numpy/core/include g++ -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > rm xmipp_test_main* > Checking MPI configuration ... > /usr/lib64/openmpi/bin/mpicxx -c -w -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -mtune=native -march=native -std=c++11 -O3 xmipp_mpi_test_main.cpp -o xmipp_mpi_test_main.o > /usr/lib64/openmpi/bin/mpicxx -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_mpi_test_main.o -o xmipp_mpi_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > rm xmipp_mpi_test_main* > /usr/lib64/openmpi/bin/mpirun -np 2 echo ' > This sentence should be printed 2 times if mpi runs fine.' > > This sentence should be printed 2 times if mpi runs fine. > > This sentence should be printed 2 times if mpi runs fine. > Checking Java configuration... > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/bin/javac Xmipp.java > rm Xmipp.java Xmipp.class > g++ -c -w -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include/linux -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_jni_test.cpp -o xmipp_jn > i_test.o rm xmipp_jni_test* > Checking CUDA configuration ... > /usr/local/cuda-10.1/bin/nvcc -c -w --x cu -D_FORCE_INLINES -Xcompiler -fPIC -ccbin g++ -std=c++11 --expt-extended-lambda -gencode=arch=compute_30,code=compute_30 -gencode=arch=compute_35,code=compute_35 -gencode=arch=compute_50,code=compute_50 -gencod > e=arch=compute_60,code=compute_60 -gencode=arch=compute_61,code=compute_61 -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_cuda_test.cpp -o xmipp_cuda_test.o /usr/local/cuda-10.1/bin/nvcc -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt > g++ -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt > rm xmipp_cuda_test* > Setting VERIFIED=True > Building Dependencies ------------------------------------- > make all > mkdir -p build/ > nvcc --cudart static -shared -link -Wno-deprecated-gpu-targets -o build/libcuFFTAdvisor.so obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTran > sform.o obj/sizeOptimizer.o obj/main.omkdir -p build/ > nvcc -o build/cuFFTAdvisor obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTransform.o obj/sizeOptimizer.o obj/main.o -lcufft -Wno-deprecated-g > pu-targets cp src/cuFFTAdvisor/build/libcuFFTAdvisor.so src/xmipp/lib/ > Compiling ------------------------------------------- > scons -j4 > scons: Reading SConscript files ... > scons: done reading SConscript files. > scons: Building targets ... > scons: `lib/libXmippCore.so' is up to date. > scons: `lib/xmippCore.so' is up to date. > scons: done building targets. > scons -j4 > scons: Reading SConscript files ... > scons: done reading SConscript files. > scons: Building targets ... > scons: `lib/libXmipp.so' is up to date. > scons: `lib/_swig_frm.so' is up to date. > scons: `lib/libXmippCuda.a' is up to date. > scons: `lib/libXmippInterfaceCuda.so' is up to date. > scons: `lib/libXmippParallelCuda.so' is up to date. > scons: `lib/libXmippParallel.so' is up to date. > g++ -o bin/xmipp_volume_from_pdb applications/programs/volume_from_pdb/volume_from_pdb_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhd > f5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_idr_xray_tomo applications/programs/idr_xray_tomo/idr_xray_tomo_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhdf5 -lh > df5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_image_separate_objects applications/programs/image_separate_objects/image_separate_objects_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion > 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_pdb_reduce_pseudoatoms applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion > 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore/usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_volume_from_pdb] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_idr_xray_tomo] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_image_separate_objects] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_pdb_reduce_pseudoatoms] Error 1 > scons: building terminated because of errors. > > Some error occurred during the compilation of 'xmipp' ('bin/xmipp_pdb_reduce_pseudoatoms'). > > Traceback (most recent call last): > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 449, in <module> > main() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 292, in main > installPluginMethods() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin > environment.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute > self._executeTargets(targetList) > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets > tgt.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute > command.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scip > ion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')Error at main: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipi > on3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') > Something went wrong running: > eval "$(/home/raozh/wtao/conda/miniconda/condabin/conda shell.bash hook)" && > conda create -n .scipion3env python=3 && > conda activate .scipion3env && > cd /home/raozh/wtao/scipion3 && > mkdir -p software/lib && > mkdir -p software/bindings && > mkdir -p software/em && > export SCIPION_HOME=/home/raozh/wtao/scipion3 && > pip install scipion-pyworkflow && > pip install scipion-app && > python -m scipion installp -p scipion-em-xmipp -j 4 > Installation cancelled. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: 王涛 <wt...@ma...> - 2020-10-03 18:48:56
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hello everyone, I got a problem while installing scipion3 with miniconda. I installed conda at first,then: pip install --user scipion-installer python3 -m scipioninstaller /path/where/you/want/scipion -j 4 then program failed in compiling module 'xmipp',and log showed that there may be some errors in linking hdf5 library,but I have hdf5 installed by conda with default channel. There is another warning about libjpeg.so at /usr/lib64 in error logs, so I think program may not find library in .scipion3env as normal,and I don't know which file should I configure.(maybe xmipp.conf or SConscript or SConstruct?) (.scipion3env) [raozh@mgmt01 scipion3]$ conda list hdf5 # packages in environment at /home/raozh/wtao/conda/miniconda/envs/.scipion3env: # # Name Version Build Channel hdf5 1.10.7 hb1b8bf9_0 Anybody got any idea about this? Thanks for any help. Tao Wang Ph.D candidate, Tsinghua University here are logs: (.scipion3env) [raozh@mgmt01 scipion3]$ python3 -m scipioninstaller /home/raozh/wtao/scipion3/ -j 4 conda detected. Favouring it. If you want a virtualenv installation cancel installation and pass --venv . WARNING: A conda environment already exists at '/home/raozh/wtao/conda/miniconda/envs/.scipion3env' Remove existing environment (y/[n])? CondaSystemExit: Exiting. Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (3.2.2) Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.0.0) Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (7.1.2) Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.7.0) Requirement already satisfied: requests<=2.23.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (2.23.0) Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.18.4) Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.2.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.2.0) Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20) Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.10) Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) Requirement already satisfied: scipion-app in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) Requirement already satisfied: scipion-em in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (3.0.3) Requirement already satisfied: outdated==0.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (0.2.0) Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (3.0.4) Requirement already satisfied: biopython==1.76 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (1.76) Requirement already satisfied: littleutils in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (0.2.2) Requirement already satisfied: requests in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (2.23.0) Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.0.0) Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.2.2) Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (1.25.10) Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20) Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7) Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1) Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2) Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0) Scipion v3.0.4 () devel >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Building scipion-em-xmipp ... /home/raozh/wtao/conda/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7rc1 Requirement already satisfied: scipion-em-xmipp==20.7rc1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (20.7rc1) Requirement already satisfied: scons in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (4.0.1) Requirement already satisfied: plotter in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (1.3.17) Requirement already satisfied: joblib in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.17.0) Requirement already satisfied: scikit-learn==0.22.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.22.1) Requirement already satisfied: peppercorn in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.6) Requirement already satisfied: setuptools in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scons->scipion-em-xmipp==20.7rc1) (49.6.0.post20200925) Requirement already satisfied: numpy>=1.11.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.18.4) Requirement already satisfied: scipy>=0.17.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.5.2) Done (0.78 seconds) Building xmippSrc-3.20.07rc ... Skipping command: wget -nv -c -O /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07rc.tgz mv -v /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz All targets exist. Skipping command: tar -xf xmippSrc-v3.20.07rc.tgz All targets exist. cd /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null Configuring ----------------------------------------- gcc detected g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include OpenCV not found rm -v xmipp_test_opencv* 'mpirun' and 'mpiexec' not found in the PATH Using '/usr/lib64/openmpi/bin'. 'mpicc' not found in the PATH Using '/usr/lib64/openmpi/bin'. 'mpicxx' not found in the PATH Using '/usr/lib64/openmpi/bin'. Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN) Using '/usr/local/cuda/bin'. CUDA-10.1.168 detected. CUDA-8.0 is recommended. Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'. Configuration completed..... Checking configuration ------------------------------ Checking compiler configuration ... g++ 4.8.5 detected g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_main.cpp -o xmipp_test_main.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include/python3.8 -I/home/raozh/wtao/c onda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/numpy/core/include g++ -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 rm xmipp_test_main* Checking MPI configuration ... /usr/lib64/openmpi/bin/mpicxx -c -w -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -mtune=native -march=native -std=c++11 -O3 xmipp_mpi_test_main.cpp -o xmipp_mpi_test_main.o /usr/lib64/openmpi/bin/mpicxx -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_mpi_test_main.o -o xmipp_mpi_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 rm xmipp_mpi_test_main* /usr/lib64/openmpi/bin/mpirun -np 2 echo ' > This sentence should be printed 2 times if mpi runs fine.' > This sentence should be printed 2 times if mpi runs fine. > This sentence should be printed 2 times if mpi runs fine. Checking Java configuration... /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/bin/javac Xmipp.java rm Xmipp.java Xmipp.class g++ -c -w -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include/linux -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_jni_test.cpp -o xmipp_jn i_test.o rm xmipp_jni_test* Checking CUDA configuration ... /usr/local/cuda-10.1/bin/nvcc -c -w --x cu -D_FORCE_INLINES -Xcompiler -fPIC -ccbin g++ -std=c++11 --expt-extended-lambda -gencode=arch=compute_30,code=compute_30 -gencode=arch=compute_35,code=compute_35 -gencode=arch=compute_50,code=compute_50 -gencod e=arch=compute_60,code=compute_60 -gencode=arch=compute_61,code=compute_61 -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_cuda_test.cpp -o xmipp_cuda_test.o /usr/local/cuda-10.1/bin/nvcc -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt g++ -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt rm xmipp_cuda_test* Setting VERIFIED=True Building Dependencies ------------------------------------- make all mkdir -p build/ nvcc --cudart static -shared -link -Wno-deprecated-gpu-targets -o build/libcuFFTAdvisor.so obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTran sform.o obj/sizeOptimizer.o obj/main.omkdir -p build/ nvcc -o build/cuFFTAdvisor obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTransform.o obj/sizeOptimizer.o obj/main.o -lcufft -Wno-deprecated-g pu-targets cp src/cuFFTAdvisor/build/libcuFFTAdvisor.so src/xmipp/lib/ Compiling ------------------------------------------- scons -j4 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: `lib/libXmippCore.so' is up to date. scons: `lib/xmippCore.so' is up to date. scons: done building targets. scons -j4 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: `lib/libXmipp.so' is up to date. scons: `lib/_swig_frm.so' is up to date. scons: `lib/libXmippCuda.a' is up to date. scons: `lib/libXmippInterfaceCuda.so' is up to date. scons: `lib/libXmippParallelCuda.so' is up to date. scons: `lib/libXmippParallel.so' is up to date. g++ -o bin/xmipp_volume_from_pdb applications/programs/volume_from_pdb/volume_from_pdb_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhd f5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_idr_xray_tomo applications/programs/idr_xray_tomo/idr_xray_tomo_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhdf5 -lh df5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_image_separate_objects applications/programs/image_separate_objects/image_separate_objects_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_pdb_reduce_pseudoatoms applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore/usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_volume_from_pdb] Error 1 /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_idr_xray_tomo] Error 1 /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_image_separate_objects] Error 1 /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_pdb_reduce_pseudoatoms] Error 1 scons: building terminated because of errors. Some error occurred during the compilation of 'xmipp' ('bin/xmipp_pdb_reduce_pseudoatoms'). Traceback (most recent call last): File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 449, in <module> main() File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 292, in main installPluginMethods() File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute command.execute() File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scip ion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')Error at main: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipi on3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') Something went wrong running: eval "$(/home/raozh/wtao/conda/miniconda/condabin/conda shell.bash hook)" && conda create -n .scipion3env python=3 && conda activate .scipion3env && cd /home/raozh/wtao/scipion3 && mkdir -p software/lib && mkdir -p software/bindings && mkdir -p software/em && export SCIPION_HOME=/home/raozh/wtao/scipion3 && pip install scipion-pyworkflow && pip install scipion-app && python -m scipion installp -p scipion-em-xmipp -j 4 Installation cancelled. |
|
From: <pc...@cn...> - 2020-10-03 06:43:17
|
<div dir='auto'>I think we have implemented that functionality. Once reviewed and approved we will release a new version with it. <div dir="auto"><br></div><div dir="auto">If you want to test it before that I can give you the command to install the patch</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 2 oct. 2020 23:20, Colin Deniston <ckd...@gm...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks for the info. Integrating the wait command in the templates somehow would definitely be useful. I'll take a better look at the python script but I'm not much of a coder and at first glance that script doesn't appear to have a way to sequentially run the protocols. Not sure how to implement that in the script myself. Also, my colors appear different from what you've mentioned, maybe because I'm using Scipion 3.0? Peach is scheduled for me, orange is running, and green is finished. Thanks for all the help!</div><br /><div class="elided-text"><div dir="ltr">On Fri, Oct 2, 2020 at 12:58 AM Pablo Conesa <<a href="mailto:pconesa@cnb.csic.es">pconesa@cnb.csic.es</a>> wrote:<br /></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex">
<div>
<p>Thanks Colin, see anwser in line.<br />
</p>
<div>On 1/10/20 23:49, Colin Deniston wrote:<br />
</div>
<blockquote>
<div>
<p>Hello,<u></u><u></u></p>
<p><u></u> <u></u></p>
<p>First off, I’m new to Scipion and have been
loving the flexibility, streaming, monitoring, and reporting
abilities of the program! However, I’m currently trying to run
a custom built workflow in Scipion 3.0.3 and I’m running into
a few issues. <u></u><u></u></p>
<p><u></u> <u></u></p>
<p>1) I don’t see in the actual .json.template
file a line to designate what ID to wait for under each
protocol (I want each job to wait for the prior job to
completely finish before running). Is this something I can
add? If so, what is the command I should use? </p>
</div>
</blockquote>
Certainly something to Implement. Jose Miguel is right about the ids
potentially been changes, but I think we can update the "wait for"
attribute too (and export it/import it). I've created and <a href="https://github.com/scipion-em/scipion-pyworkflow/issues/151">issue</a>
and will look at it: <br />
<blockquote>
<div>
<p><u></u><u></u></p>
<p>2) When I try and circumvent that by simply
typing the ID in the GUI once the workflow is loaded (in the
“wait for” box of each protocol), nothing seems to wait. They
all run while the previous job is still going. Am I doing
something wrong? I’ve been entering them as just the ID number
like “432” but should they be entered differently? Also, I see
multiple IDs for the same job/protocol under different menus,
not sure if that is a bug or not or whether it is maybe
related to the issue of jobs not waiting. </p>
</div>
</blockquote>
<p>The expected behavior is all should be "scheduled" (orange). This
does not mean they are running, but they are actively checking is
they can start once all validation passes (wait for should be part
of the validation)</p>
<p>Do the box with the "wait for" turns orange (scheduled,this would
be correct) or green (running, thus not waiting)?<br />
</p>
<blockquote>
<div>
<p><u></u><u></u></p>
<p><u></u> <u></u></p>
<p>Any feedback would be helpful, my end goal
is just to make a reproducible workflow that can be loaded and
run on multiple Appoferritin calibration datasets all the way
to 3D refinement without any user intervention. However, at
the moment one job will try to run too soon and fail and then
lead to a cascade of downstream jobs failing. Thanks!<u></u><u></u></p>
<p><u></u> <u></u></p>
<p><b><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 );background:white">Colin
Deniston</span></b><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )"><br />
<span style="background:white">Principal Scientist I</span><br />
<br />
</span><u></u><u></u></p>
<p style="background:white"><b><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 47 , 84 , 150 )">GNF
BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF<u></u><u></u></span></b></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">Novartis
Institutes for Biomed.Research, Inc.<u></u><u></u></span></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">10675
John Jay Hopkins Drive<u></u><u></u></span></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">GNF
Business<u></u><u></u></span></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">San
Diego, CA 92121<u></u><u></u></span></p>
<p><u></u> <u></u></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">T
+1 (858) 332-4750<u></u><u></u></span></p>
<p><a href="mailto:cdeniston@gnf.org"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 47 , 84 , 150 );background:white">cdeniston@gnf.org</span></a><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )"><br />
<br />
</span><a href="https://www.novartis.com/"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 4 , 96 , 169 );background:white;text-decoration:none"><img style="width:1.3541in;height:0.2395in" src="cid:174eaaf55084cff311" alt="https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png" width="130" height="23" border="0" /></span></a><u></u><u></u></p>
<p><u></u> <u></u></p>
</div>
<br />
<fieldset></fieldset>
<br />
<fieldset></fieldset>
<pre>_______________________________________________
scipion-users mailing list
<a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a>
<a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a>
</pre>
</blockquote>
<div>-- <br />
Pablo Conesa - <strong>Madrid <a href="http://scipion.i2pc.es">Scipion</a>
team</strong></div>
</div>
_______________________________________________<br />
scipion-users mailing list<br />
<a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a><br />
<a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><br />
</blockquote></div>
</blockquote></div><br></div> |
|
From: Colin D. <ckd...@gm...> - 2020-10-02 21:20:56
|
Thanks for the info. Integrating the wait command in the templates somehow would definitely be useful. I'll take a better look at the python script but I'm not much of a coder and at first glance that script doesn't appear to have a way to sequentially run the protocols. Not sure how to implement that in the script myself. Also, my colors appear different from what you've mentioned, maybe because I'm using Scipion 3.0? Peach is scheduled for me, orange is running, and green is finished. Thanks for all the help! On Fri, Oct 2, 2020 at 12:58 AM Pablo Conesa <pc...@cn...> wrote: > Thanks Colin, see anwser in line. > On 1/10/20 23:49, Colin Deniston wrote: > > Hello, > > > > First off, I’m new to Scipion and have been loving the flexibility, > streaming, monitoring, and reporting abilities of the program! However, I’m > currently trying to run a custom built workflow in Scipion 3.0.3 and I’m > running into a few issues. > > > > 1) I don’t see in the actual .json.template file a line to designate what > ID to wait for under each protocol (I want each job to wait for the prior > job to completely finish before running). Is this something I can add? If > so, what is the command I should use? > > Certainly something to Implement. Jose Miguel is right about the ids > potentially been changes, but I think we can update the "wait for" > attribute too (and export it/import it). I've created and issue > <https://github.com/scipion-em/scipion-pyworkflow/issues/151> and will > look at it: > > 2) When I try and circumvent that by simply typing the ID in the GUI once > the workflow is loaded (in the “wait for” box of each protocol), nothing > seems to wait. They all run while the previous job is still going. Am I > doing something wrong? I’ve been entering them as just the ID number like > “432” but should they be entered differently? Also, I see multiple IDs for > the same job/protocol under different menus, not sure if that is a bug or > not or whether it is maybe related to the issue of jobs not waiting. > > The expected behavior is all should be "scheduled" (orange). This does not > mean they are running, but they are actively checking is they can start > once all validation passes (wait for should be part of the validation) > > Do the box with the "wait for" turns orange (scheduled,this would be > correct) or green (running, thus not waiting)? > > > > Any feedback would be helpful, my end goal is just to make a reproducible > workflow that can be loaded and run on multiple Appoferritin calibration > datasets all the way to 3D refinement without any user intervention. > However, at the moment one job will try to run too soon and fail and then > lead to a cascade of downstream jobs failing. Thanks! > > > > *Colin Deniston* > Principal Scientist I > > *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF* > > Novartis Institutes for Biomed.Research, Inc. > > 10675 John Jay Hopkins Drive > > GNF Business > > San Diego, CA 92121 > > > > T +1 (858) 332-4750 > > cde...@gn... > > [image: https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png] > <https://www.novartis.com/> > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2020-10-02 11:35:02
|
Thanks Wolfgang!
There is something on our side that I think is not smooth when updating
xmipp. I think we need to review this case.
On 2/10/20 12:43, Lugmayr, Wolfgang wrote:
> Hi,
>
> I fixed it. I deleted the extracted xmipp b1 version and put some path
> to the scipion module.
> Now the error disappeared.
>
> $ m show scipion
> -------------------------------------------------------------------
> /beegfs/cssb/software/modulefiles/em/scipion/3.0-dev:
>
> module-whatis development version, default build
> module load deps/gcc8-openmpi4-cuda10
> prepend-path PATH /beegfs/cssb/software/em/scipion/3.0/devel
> setenv SCIPION_HOME /beegfs/cssb/software/em/scipion/3.0/devel
> prepend-path PYTHONPATH
> /beegfs/cssb/software/em/scipion/3.0/devel/software/em/xmipp/pylib
> prepend-path PYTHONPATH
> /beegfs/cssb/software/em/scipion/3.0/devel/software/em/xmipp/bindings/python
>
>
> Cheers,
> Wolfgang
>
>
> ------------------------------------------------------------------------
> *From: *"Lugmayr, Wolfgang" <w.l...@uk...>
> *To: *"Mailing list for Scipion users"
> <sci...@li...>
> *Sent: *Friday, 2 October, 2020 12:28:34
> *Subject: *Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure
>
> Hi,
>
> in software/em xmipp pointed to
> xmipp -> xmippSrc-v3.20.07b1/build/
> I fixed it by hand to
> xmipp -> xmippSrc-v3.20.07rc/build/
> but the message still comes.
>
> $ m show scipion
> -------------------------------------------------------------------
> /beegfs/cssb/software/modulefiles/em/scipion/3.0-dev:
>
> module-whatis development version, default build
> module load deps/gcc8-openmpi4-cuda10
> prepend-path PATH /beegfs/cssb/software/em/scipion/3.0/devel
> setenv SCIPION_HOME /beegfs/cssb/software/em/scipion/3.0/devel
> -------------------------------------------------------------------
>
> $ m load scipion
> CUDA 10.1 loaded
>
> $ echo $LD_LIBRARY_PATH
> /beegfs/cssb/software/devel/gcc/8.4.0/lib64:/beegfs/cssb/software/devel/mpc/1.0.3/lib:/beegfs/cssb/software/devel/mpfr/3.1.4/lib:/beegfs/cssb/software/devel/hwloc/2.1.0/lib:/beegfs/cssb/software/devel/ucx/1.8.0/lib:/beegfs/cssb/software/devel/openmpi/4.0.3/lib:/usr/local/cuda-10.1/lib64
>
> $ echo $PATHONPATH
>
> $ scipion3
> Scipion v3.0.3 () devel
>
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin
> manager window)
>
>
> > error when importing from xmipp3.protocols: cannot import name
> 'isMdEmpty' from 'xmipp3.base'
> (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py)
> File
> "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py",
> line 44, in <module>
> Check the plugin manager (Configuration->Plugins in Scipion manager
> window)
> or use 'scipion installp --help --checkUpdates' in the command line
> to check for upgrades,
> it could be a versions compatibility issue.
>
> Cheers,
> Wolfgang
>
>
> ------------------------------------------------------------------------
> *From: *"Pablo Conesa" <pc...@cn...>
> *To: *"Mailing list for Scipion users"
> <sci...@li...>
> *Sent: *Friday, 2 October, 2020 11:30:00
> *Subject: *Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure
>
> Hi Wolfgang.
>
> This error also happens (actually yesterday) when there is something
> in PYTHONPATH variable pointing to old scipion2 paths. Could this be
> your case?
>
> Could you send the output of:
>
> echo $LD_LIBRARY_PATH
>
> echo $PYTHONPATH
>
>
> NOTE: If you look inside "scipion3" launcher it it a small python
> script setting up the environment and is "conserving" the content of
> both variables. To be honest, I do not see a strong reason for this or
> the opposite, but if this is the case, not conserving the values would
> work:
>
> You should have this:
>
> os.environ["LD_LIBRARY_PATH"] =
> ":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome,
> "software", "lib")])
> os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""),
> join(scipionHome, "software", "bindings")])
>
> Suggested change:
>
> os.environ["LD_LIBRARY_PATH"] = join(scipionHome, "software", "lib")
> os.environ["PYTHONPATH"] = join(scipionHome, "software", "bindings")
>
> But not sure if this is your case.
>
>
> On 2/10/20 10:49, Lugmayr, Wolfgang wrote:
>
> Hi,
>
> I have a problem with xmipp_cuda_movie_alignment_correlation dying with Signal 6 and before posting I tried to update xmipp yesterday.
>
> I updated xmipp via the plugin manager (together with the scipion-em-tomo package).
> Now i get the error message below.
>
> Starting "scipion3 last" prints the following:_
>
> $ scipion3
> Scipion v3.0.3 () devel
>
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
>
>
> > error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py)
> File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
> Check the plugin manager (Configuration->Plugins in Scipion manager window)
> or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
> it could be a versions compatibility issue.
>
> Here are the xmipp infos:
> scipion-em-tomo 3.0.6 [X]
> scipion-em-xmipp 20.7rc1 [X]
> scipion-em-xmipp2 3.0.0 [X]
>
> I think the hint should be now:
> scipion3 installp --help --checkUpdates
>
> Cheers,
> Wolfgang
>
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Lugmayr, W. <w.l...@uk...> - 2020-10-02 10:56:30
|
Hi,
I fixed it. I deleted the extracted xmipp b1 version and put some path to the scipion module.
Now the error disappeared.
$ m show scipion
-------------------------------------------------------------------
/beegfs/cssb/software/modulefiles/em/scipion/3.0-dev:
module-whatis development version, default build
module load deps/gcc8-openmpi4-cuda10
prepend-path PATH /beegfs/cssb/software/em/scipion/3.0/devel
setenv SCIPION_HOME /beegfs/cssb/software/em/scipion/3.0/devel
prepend-path PYTHONPATH /beegfs/cssb/software/em/scipion/3.0/devel/software/em/xmipp/pylib
prepend-path PYTHONPATH /beegfs/cssb/software/em/scipion/3.0/devel/software/em/xmipp/bindings/python
Cheers,
Wolfgang
From: "Lugmayr, Wolfgang" <w.l...@uk...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Friday, 2 October, 2020 12:28:34
Subject: Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure
Hi,
in software/em xmipp pointed to
xmipp -> xmippSrc-v3.20.07b1/build/
I fixed it by hand to
xmipp -> xmippSrc-v3.20.07rc/build/
but the message still comes.
$ m show scipion
-------------------------------------------------------------------
/beegfs/cssb/software/modulefiles/em/scipion/3.0-dev:
module-whatis development version, default build
module load deps/gcc8-openmpi4-cuda10
prepend-path PATH /beegfs/cssb/software/em/scipion/3.0/devel
setenv SCIPION_HOME /beegfs/cssb/software/em/scipion/3.0/devel
-------------------------------------------------------------------
$ m load scipion
CUDA 10.1 loaded
$ echo $LD_LIBRARY_PATH
/beegfs/cssb/software/devel/gcc/8.4.0/lib64:/beegfs/cssb/software/devel/mpc/1.0.3/lib:/beegfs/cssb/software/devel/mpfr/3.1.4/lib:/beegfs/cssb/software/devel/hwloc/2.1.0/lib:/beegfs/cssb/software/devel/ucx/1.8.0/lib:/beegfs/cssb/software/devel/openmpi/4.0.3/lib:/usr/local/cuda-10.1/lib64
$ echo $PATHONPATH
$ scipion3
Scipion v3.0.3 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
> error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py)
File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
Cheers,
Wolfgang
From: "Pablo Conesa" <pc...@cn...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Friday, 2 October, 2020 11:30:00
Subject: Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure
Hi Wolfgang.
This error also happens (actually yesterday) when there is something in PYTHONPATH variable pointing to old scipion2 paths. Could this be your case?
Could you send the output of:
echo $LD_LIBRARY_PATH
echo $PYTHONPATH
NOTE: If you look inside "scipion3" launcher it it a small python script setting up the environment and is "conserving" the content of both variables. To be honest, I do not see a strong reason for this or the opposite, but if this is the case, not conserving the values would work:
You should have this:
os.environ["LD_LIBRARY_PATH"] = ":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome, "software", "lib")])
os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""), join(scipionHome, "software", "bindings")])
Suggested change:
os.environ["LD_LIBRARY_PATH"] = join(scipionHome, "software", "lib")
os.environ["PYTHONPATH"] = join(scipionHome, "software", "bindings")
But not sure if this is your case.
On 2/10/20 10:49, Lugmayr, Wolfgang wrote:
Hi,
I have a problem with xmipp_cuda_movie_alignment_correlation dying with Signal 6 and before posting I tried to update xmipp yesterday.
I updated xmipp via the plugin manager (together with the scipion-em-tomo package).
Now i get the error message below.
Starting "scipion3 last" prints the following:_
$ scipion3
Scipion v3.0.3 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
> error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py)
File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
Here are the xmipp infos:
scipion-em-tomo 3.0.6 [X]
scipion-em-xmipp 20.7rc1 [X]
scipion-em-xmipp2 3.0.0 [X]
I think the hint should be now:
scipion3 installp --help --checkUpdates
Cheers,
Wolfgang
--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Lugmayr, W. <w.l...@uk...> - 2020-10-02 10:29:10
|
Hi,
in software/em xmipp pointed to
xmipp -> xmippSrc-v3.20.07b1/build/
I fixed it by hand to
xmipp -> xmippSrc-v3.20.07rc/build/
but the message still comes.
$ m show scipion
-------------------------------------------------------------------
/beegfs/cssb/software/modulefiles/em/scipion/3.0-dev:
module-whatis development version, default build
module load deps/gcc8-openmpi4-cuda10
prepend-path PATH /beegfs/cssb/software/em/scipion/3.0/devel
setenv SCIPION_HOME /beegfs/cssb/software/em/scipion/3.0/devel
-------------------------------------------------------------------
$ m load scipion
CUDA 10.1 loaded
$ echo $LD_LIBRARY_PATH
/beegfs/cssb/software/devel/gcc/8.4.0/lib64:/beegfs/cssb/software/devel/mpc/1.0.3/lib:/beegfs/cssb/software/devel/mpfr/3.1.4/lib:/beegfs/cssb/software/devel/hwloc/2.1.0/lib:/beegfs/cssb/software/devel/ucx/1.8.0/lib:/beegfs/cssb/software/devel/openmpi/4.0.3/lib:/usr/local/cuda-10.1/lib64
$ echo $PATHONPATH
$ scipion3
Scipion v3.0.3 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
> error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py)
File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
Cheers,
Wolfgang
From: "Pablo Conesa" <pc...@cn...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Friday, 2 October, 2020 11:30:00
Subject: Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure
Hi Wolfgang.
This error also happens (actually yesterday) when there is something in PYTHONPATH variable pointing to old scipion2 paths. Could this be your case?
Could you send the output of:
echo $LD_LIBRARY_PATH
echo $PYTHONPATH
NOTE: If you look inside "scipion3" launcher it it a small python script setting up the environment and is "conserving" the content of both variables. To be honest, I do not see a strong reason for this or the opposite, but if this is the case, not conserving the values would work:
You should have this:
os.environ["LD_LIBRARY_PATH"] = ":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome, "software", "lib")])
os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""), join(scipionHome, "software", "bindings")])
Suggested change:
os.environ["LD_LIBRARY_PATH"] = join(scipionHome, "software", "lib")
os.environ["PYTHONPATH"] = join(scipionHome, "software", "bindings")
But not sure if this is your case.
On 2/10/20 10:49, Lugmayr, Wolfgang wrote:
Hi,
I have a problem with xmipp_cuda_movie_alignment_correlation dying with Signal 6 and before posting I tried to update xmipp yesterday.
I updated xmipp via the plugin manager (together with the scipion-em-tomo package).
Now i get the error message below.
Starting "scipion3 last" prints the following:_
$ scipion3
Scipion v3.0.3 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
> error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py)
File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
Here are the xmipp infos:
scipion-em-tomo 3.0.6 [X]
scipion-em-xmipp 20.7rc1 [X]
scipion-em-xmipp2 3.0.0 [X]
I think the hint should be now:
scipion3 installp --help --checkUpdates
Cheers,
Wolfgang
--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: David M. <dma...@cn...> - 2020-10-02 10:19:11
|
Hi Wolfgang, After updating the scipion-em-xmipp plugin, it is necessary to install also the xmippSrc-3.20.07rc1 bundle using the plugin manager or via *scipion3 installb xmippSrc -j 8* Also, you can check scipion3 config -p xmipp3 it prints the XMIPP_HOME detected (usually ...scipion3/software/em/xmipp) , then check that path via ls -l <XMIPP_HOME> # replace <XMIPP_HOME> for your value it should be a link pointing to xmipp-3.20.07rc1/build Thanks for reporting, Cheers. <http://ucm.es/> *_____Dr. David Maluenda Niubó* dma...@cn... - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> BioComputing Unit <http://biocomputingunit.es/> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Fri, Oct 2, 2020 at 11:30 AM Pablo Conesa <pc...@cn...> wrote: > Hi Wolfgang. > > This error also happens (actually yesterday) when there is something in > PYTHONPATH variable pointing to old scipion2 paths. Could this be your case? > > Could you send the output of: > > echo $LD_LIBRARY_PATH > > echo $PYTHONPATH > > > NOTE: If you look inside "scipion3" launcher it it a small python script > setting up the environment and is "conserving" the content of both > variables. To be honest, I do not see a strong reason for this or the > opposite, but if this is the case, not conserving the values would work: > > You should have this: > > os.environ["LD_LIBRARY_PATH"] = > ":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome, > "software", "lib")]) > os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""), > join(scipionHome, "software", "bindings")]) > > Suggested change: > > os.environ["LD_LIBRARY_PATH"] = join(scipionHome, "software", "lib") > os.environ["PYTHONPATH"] = join(scipionHome, "software", "bindings") > > But not sure if this is your case. > > > On 2/10/20 10:49, Lugmayr, Wolfgang wrote: > > Hi, > > I have a problem with xmipp_cuda_movie_alignment_correlation dying with Signal 6 and before posting I tried to update xmipp yesterday. > > I updated xmipp via the plugin manager (together with the scipion-em-tomo package). > Now i get the error message below. > > Starting "scipion3 last" prints the following:_ > > $ scipion3 > Scipion v3.0.3 () devel > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) > > > > error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py) > File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager window) > or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, > it could be a versions compatibility issue. > > Here are the xmipp infos: > scipion-em-tomo 3.0.6 [X] > scipion-em-xmipp 20.7rc1 [X] > scipion-em-xmipp2 3.0.0 [X] > > I think the hint should be now: > scipion3 installp --help --checkUpdates > > Cheers, > Wolfgang > > > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2020-10-02 09:30:17
|
Hi Wolfgang.
This error also happens (actually yesterday) when there is something in
PYTHONPATH variable pointing to old scipion2 paths. Could this be your case?
Could you send the output of:
echo $LD_LIBRARY_PATH
echo $PYTHONPATH
NOTE: If you look inside "scipion3" launcher it it a small python script
setting up the environment and is "conserving" the content of both
variables. To be honest, I do not see a strong reason for this or the
opposite, but if this is the case, not conserving the values would work:
You should have this:
os.environ["LD_LIBRARY_PATH"] =
":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome,
"software", "lib")])
os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""),
join(scipionHome, "software", "bindings")])
Suggested change:
os.environ["LD_LIBRARY_PATH"] = join(scipionHome, "software", "lib")
os.environ["PYTHONPATH"] = join(scipionHome, "software", "bindings")
But not sure if this is your case.
On 2/10/20 10:49, Lugmayr, Wolfgang wrote:
> Hi,
>
> I have a problem with xmipp_cuda_movie_alignment_correlation dying with Signal 6 and before posting I tried to update xmipp yesterday.
>
> I updated xmipp via the plugin manager (together with the scipion-em-tomo package).
> Now i get the error message below.
>
> Starting "scipion3 last" prints the following:_
>
> $ scipion3
> Scipion v3.0.3 () devel
>
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
>
>
> > error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py)
> File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
> Check the plugin manager (Configuration->Plugins in Scipion manager window)
> or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
> it could be a versions compatibility issue.
>
> Here are the xmipp infos:
> scipion-em-tomo 3.0.6 [X]
> scipion-em-xmipp 20.7rc1 [X]
> scipion-em-xmipp2 3.0.0 [X]
>
> I think the hint should be now:
> scipion3 installp --help --checkUpdates
>
> Cheers,
> Wolfgang
>
>
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Lugmayr, W. <w.l...@uk...> - 2020-10-02 08:50:02
|
Hi, I have a problem with xmipp_cuda_movie_alignment_correlation dying with Signal 6 and before posting I tried to update xmipp yesterday. I updated xmipp via the plugin manager (together with the scipion-em-tomo package). Now i get the error message below. Starting "scipion3 last" prints the following:_ $ scipion3 Scipion v3.0.3 () devel >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) > error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py) File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module> Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue. Here are the xmipp infos: scipion-em-tomo 3.0.6 [X] scipion-em-xmipp 20.7rc1 [X] scipion-em-xmipp2 3.0.0 [X] I think the hint should be now: scipion3 installp --help --checkUpdates Cheers, Wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 22607 Hamburg, Germany Tel.: +49 40 8998-87652 Email: wol...@cs... http://www.cssb-hamburg.de/ |
|
From: Pablo C. <pc...@cn...> - 2020-10-02 07:58:40
|
Thanks Colin, see anwser in line. On 1/10/20 23:49, Colin Deniston wrote: > > Hello, > > First off, I’m new to Scipion and have been loving the flexibility, > streaming, monitoring, and reporting abilities of the program! > However, I’m currently trying to run a custom built workflow in > Scipion 3.0.3 and I’m running into a few issues. > > 1) I don’t see in the actual .json.template file a line to designate > what ID to wait for under each protocol (I want each job to wait for > the prior job to completely finish before running). Is this something > I can add? If so, what is the command I should use? > Certainly something to Implement. Jose Miguel is right about the ids potentially been changes, but I think we can update the "wait for" attribute too (and export it/import it). I've created and issue <https://github.com/scipion-em/scipion-pyworkflow/issues/151> and will look at it: > > 2) When I try and circumvent that by simply typing the ID in the GUI > once the workflow is loaded (in the “wait for” box of each protocol), > nothing seems to wait. They all run while the previous job is still > going. Am I doing something wrong? I’ve been entering them as just the > ID number like “432” but should they be entered differently? Also, I > see multiple IDs for the same job/protocol under different menus, not > sure if that is a bug or not or whether it is maybe related to the > issue of jobs not waiting. > The expected behavior is all should be "scheduled" (orange). This does not mean they are running, but they are actively checking is they can start once all validation passes (wait for should be part of the validation) Do the box with the "wait for" turns orange (scheduled,this would be correct) or green (running, thus not waiting)? > Any feedback would be helpful, my end goal is just to make a > reproducible workflow that can be loaded and run on multiple > Appoferritin calibration datasets all the way to 3D refinement without > any user intervention. However, at the moment one job will try to run > too soon and fail and then lead to a cascade of downstream jobs > failing. Thanks! > > *Colin Deniston* > Principal Scientist I > > *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF* > > Novartis Institutes for Biomed.Research, Inc. > > 10675 John Jay Hopkins Drive > > GNF Business > > San Diego, CA 92121 > > T +1 (858) 332-4750 > > cde...@gn... <mailto:cde...@gn...> > > https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png > <https://www.novartis.com/> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Jose M. de la R. T. <del...@gm...> - 2020-10-02 07:11:03
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Hi Colin, Thanks for reaching out. Regarding your question, it is not possible to set the waiting ID from the workflow template. The reason for this is that the ID shown in the template .json file might change when imported into the project (e.g other objects might already have that ID). But your goal of launching a whole pipeline where one job waits for the other is doable via the Python API. It might require some Python coding, but not really complex. You can get an idea with the following scripts that launch a workflow from a json file (almost the same that you want to achieve): https://github.com/I2PC/scipion-scripts/blob/master/run_workflow.py Please let me know if you have any questions. Kind regards, Jose Miguel On Fri, Oct 2, 2020 at 9:03 AM Colin Deniston <cde...@gn...> wrote: > Hello, > > > > First off, I’m new to Scipion and have been loving the flexibility, > streaming, monitoring, and reporting abilities of the program! However, I’m > currently trying to run a custom built workflow in Scipion 3.0.3 and I’m > running into a few issues. > > > > 1) I don’t see in the actual .json.template file a line to designate what > ID to wait for under each protocol (I want each job to wait for the prior > job to completely finish before running). Is this something I can add? If > so, what is the command I should use? > > 2) When I try and circumvent that by simply typing the ID in the GUI once > the workflow is loaded (in the “wait for” box of each protocol), nothing > seems to wait. They all run while the previous job is still going. Am I > doing something wrong? I’ve been entering them as just the ID number like > “432” but should they be entered differently? Also, I see multiple IDs for > the same job/protocol under different menus, not sure if that is a bug or > not or whether it is maybe related to the issue of jobs not waiting. > > > > Any feedback would be helpful, my end goal is just to make a reproducible > workflow that can be loaded and run on multiple Appoferritin calibration > datasets all the way to 3D refinement without any user intervention. > However, at the moment one job will try to run too soon and fail and then > lead to a cascade of downstream jobs failing. Thanks! > > > > *Colin Deniston* > Principal Scientist I > > *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF* > > Novartis Institutes for Biomed.Research, Inc. > > 10675 John Jay Hopkins Drive > > GNF Business > > San Diego, CA 92121 > > > > T +1 (858) 332-4750 > > cde...@gn... > > [image: https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png] > <https://www.novartis.com/> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Colin D. <cde...@gn...> - 2020-10-02 01:23:10
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Hello, First off, I'm new to Scipion and have been loving the flexibility, streaming, monitoring, and reporting abilities of the program! However, I'm currently trying to run a custom built workflow in Scipion 3.0.3 and I'm running into a few issues. 1) I don't see in the actual .json.template file a line to designate what ID to wait for under each protocol (I want each job to wait for the prior job to completely finish before running). Is this something I can add? If so, what is the command I should use? 2) When I try and circumvent that by simply typing the ID in the GUI once the workflow is loaded (in the "wait for" box of each protocol), nothing seems to wait. They all run while the previous job is still going. Am I doing something wrong? I've been entering them as just the ID number like "432" but should they be entered differently? Also, I see multiple IDs for the same job/protocol under different menus, not sure if that is a bug or not or whether it is maybe related to the issue of jobs not waiting. Any feedback would be helpful, my end goal is just to make a reproducible workflow that can be loaded and run on multiple Appoferritin calibration datasets all the way to 3D refinement without any user intervention. However, at the moment one job will try to run too soon and fail and then lead to a cascade of downstream jobs failing. Thanks! Colin Deniston Principal Scientist I GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF Novartis Institutes for Biomed.Research, Inc. 10675 John Jay Hopkins Drive GNF Business San Diego, CA 92121 T +1 (858) 332-4750 cde...@gn...<mailto:cde...@gn...> [https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png]<https://www.novartis.com/> |
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From: Pablo C. <pc...@cn...> - 2020-09-30 07:44:11
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Thanks Khaja, All seems right providing you are on a centOS "like" machine. Is there anything printed in the console, any error message? when yo click on de "Analyze result" button? Could you please send the output of: ./scipion python -m pip list All the best, Pablo. On 30/9/20 7:01, khaja faisal tarique wrote: > Dear Pablo > > I checked it. > > Following are the binaries: > > Do you see anything missing here ? Is there anything wrong here ? > > Another question: What is the most stable version of the Scipion > available?. I could see Scipion 3.0 is also released. > > Scipion v2.0 (2019-04-23) Diocletian > > >>>>> python > /apps/SCIPION/scipion/pyworkflow/install/install-plugin.py > /apps/SCIPION/scipion/scipion installb > /apps/SCIPION/scipion/software/lib/python2.7/importlib/__init__.py:37: > CryptographyDeprecationWarning: Python 2 is no longer supported by the > Python core team. Support for it is now deprecated in cryptography, > and will be removed in a future release. > __import__(name) > Using TensorFlow backend. > WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda > being in the PATH > WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda > being in the PATH > WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda > being in the PATH > usage: /apps/SCIPION/scipion/scipion installb [-h] binName1 > binName2-1.2.3 binName3 ... > > positional arguments: > binName(s) The name(s) of the bins we want install, optionally with > version in the form name-version. If no version is > specified, > will install the last one. > > optional arguments: > -h, --help show help > -j j Number of CPUs to use for compilation > > Example: /apps/SCIPION/scipion/scipion installb ctffind4 unblur-1.0.15 > > Available binaries: ([ ] not installed, [X] seems already installed) > bsoft 1.8.8 [ ] 1.9.0 [X] > chimera 1.13.1 [ ] > cryoEF 1.1.0 [X] > cryolo 1.6.1 [ ] > cryolo_model 202002_N63 [X] 201910 [ ] > cryolo_negstain_model 20190226 [ ] > ctffind 3.6 [X] > ctffind4 4.0.15 [ ] 4.1.5 [ ] 4.1.8 [ ] 4.1.10 [X] > 4.1.13 [X] > deepLearningToolkit 0.1 [ ] > dogpicker 0.2.1.1 [X] > eman 2.21 [ ] 2.3 [X] > frealign 9.07 [X] > gctf 1.06 [ ] 1.18 [X] > janni_model 20190703 [X] > locscale 0.1 [X] > mag_distortion 1.0.1 [X] > maxit 10.1 [ ] > motioncor2 1.2.3 [ ] 1.2.6 [ ] 1.3.0 [X] > nma 1.2 [ ] 2.0 [X] > nysbc3DFSC 2.5 [X] 3.0 [ ] > powerfit 2.0 [ ] > relion 1.4 [ ] 1.4f [ ] 2.0 [ ] 2.1 [ ] > 3.0 [X] > resmap 1.95 [X] > simple 2.1 [X] > spider 25.02 [X] > summovie 1.0.2 [X] > topaz 0.2.1 [X] > unblur 1.0.15 [ ] 1.0.2 [X] > xmippBin_Centos 3.19.04 [X] > xmippBin_Debian 3.19.04 [ ] > > On Tue, Sep 29, 2020 at 5:23 PM Pablo Conesa <pc...@cn... > <mailto:pc...@cn...>> wrote: > > Hi, is this Scipion2? > > If so, have you installed xmipp plugin? > > To now that try: > > ./scipion installb > > you should see xmipp binaries listed. > > On 29/9/20 13:23, khaja faisal tarique wrote: >> Hello everyone >> >> I just installed the scipion software and while running it I am >> noticing that the Analyze Results (red eye) is not working. The >> window is not popping up to select the micrographs after ctf >> correction or for manual picking. Any idea what is wrong with this? >> >> -- >> Faisal Tarique Khaja >> Research Associate >> Indian Institute of Science >> Bangalore, India >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > -- > Faisal Tarique Khaja > Research Associate > Indian Institute of Science > Bangalore, India > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: khaja f. t. <kha...@gm...> - 2020-09-30 05:01:35
|
Dear Pablo
I checked it.
Following are the binaries:
Do you see anything missing here ? Is there anything wrong here ?
Another question: What is the most stable version of the Scipion
available?. I could see Scipion 3.0 is also released.
Scipion v2.0 (2019-04-23) Diocletian
>>>>> python /apps/SCIPION/scipion/pyworkflow/install/install-plugin.py
/apps/SCIPION/scipion/scipion installb
/apps/SCIPION/scipion/software/lib/python2.7/importlib/__init__.py:37:
CryptographyDeprecationWarning: Python 2 is no longer supported by the
Python core team. Support for it is now deprecated in cryptography, and
will be removed in a future release.
__import__(name)
Using TensorFlow backend.
WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda
being in the PATH
WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda
being in the PATH
WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda
being in the PATH
usage: /apps/SCIPION/scipion/scipion installb [-h] binName1 binName2-1.2.3
binName3 ...
positional arguments:
binName(s) The name(s) of the bins we want install, optionally with
version in the form name-version. If no version is specified,
will install the last one.
optional arguments:
-h, --help show help
-j j Number of CPUs to use for compilation
Example: /apps/SCIPION/scipion/scipion installb ctffind4 unblur-1.0.15
Available binaries: ([ ] not installed, [X] seems already installed)
bsoft 1.8.8 [ ] 1.9.0 [X]
chimera 1.13.1 [ ]
cryoEF 1.1.0 [X]
cryolo 1.6.1 [ ]
cryolo_model 202002_N63 [X] 201910 [ ]
cryolo_negstain_model 20190226 [ ]
ctffind 3.6 [X]
ctffind4 4.0.15 [ ] 4.1.5 [ ] 4.1.8 [ ] 4.1.10 [X]
4.1.13 [X]
deepLearningToolkit 0.1 [ ]
dogpicker 0.2.1.1 [X]
eman 2.21 [ ] 2.3 [X]
frealign 9.07 [X]
gctf 1.06 [ ] 1.18 [X]
janni_model 20190703 [X]
locscale 0.1 [X]
mag_distortion 1.0.1 [X]
maxit 10.1 [ ]
motioncor2 1.2.3 [ ] 1.2.6 [ ] 1.3.0 [X]
nma 1.2 [ ] 2.0 [X]
nysbc3DFSC 2.5 [X] 3.0 [ ]
powerfit 2.0 [ ]
relion 1.4 [ ] 1.4f [ ] 2.0 [ ] 2.1 [ ]
3.0 [X]
resmap 1.95 [X]
simple 2.1 [X]
spider 25.02 [X]
summovie 1.0.2 [X]
topaz 0.2.1 [X]
unblur 1.0.15 [ ] 1.0.2 [X]
xmippBin_Centos 3.19.04 [X]
xmippBin_Debian 3.19.04 [ ]
On Tue, Sep 29, 2020 at 5:23 PM Pablo Conesa <pc...@cn...> wrote:
> Hi, is this Scipion2?
>
> If so, have you installed xmipp plugin?
>
> To now that try:
>
> ./scipion installb
>
> you should see xmipp binaries listed.
> On 29/9/20 13:23, khaja faisal tarique wrote:
>
> Hello everyone
>
> I just installed the scipion software and while running it I am noticing
> that the Analyze Results (red eye) is not working. The window is not
> popping up to select the micrographs after ctf correction or for manual
> picking. Any idea what is wrong with this?
>
> --
> Faisal Tarique Khaja
> Research Associate
> Indian Institute of Science
> Bangalore, India
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
--
Faisal Tarique Khaja
Research Associate
Indian Institute of Science
Bangalore, India
|
|
From: Pablo C. <pc...@cn...> - 2020-09-29 11:52:44
|
Hi, is this Scipion2? If so, have you installed xmipp plugin? To now that try: ./scipion installb you should see xmipp binaries listed. On 29/9/20 13:23, khaja faisal tarique wrote: > Hello everyone > > I just installed the scipion software and while running it I am > noticing that the Analyze Results (red eye) is not working. The window > is not popping up to select the micrographs after ctf correction or > for manual picking. Any idea what is wrong with this? > > -- > Faisal Tarique Khaja > Research Associate > Indian Institute of Science > Bangalore, India > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: khaja f. t. <kha...@gm...> - 2020-09-29 11:24:02
|
Hello everyone I just installed the scipion software and while running it I am noticing that the Analyze Results (red eye) is not working. The window is not popping up to select the micrographs after ctf correction or for manual picking. Any idea what is wrong with this? -- Faisal Tarique Khaja Research Associate Indian Institute of Science Bangalore, India |
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From: Pablo C. <pc...@cn...> - 2020-09-28 11:17:54
|
No, it should update those 3 packages, or at least that was the intention, only if -dry is passed it will just warn. I've checked with your versions and you are right. This is wrong and not the intended behavior. We have published an update, but for those already having the "any non updatable package" Wolfgan's method will work. A more direct way would be: *scipion3 python -m pip install scipion-app==3.0.3* Once in 3.0.3, "scipion3 update" should work as Wolfgang and we expected. Thanks a lot Wolfgang. On 28/9/20 10:26, Lugmayr, Wolfgang wrote: > Hi, > > Is this intended that the update command just prints information? > I thought it would update the core packages. > > $ scipion3 update > Scipion v3.0.1 () devel > Scipion is up to date. > The package scipion-pyworkflow is out of date. Your version is 3.0.3, the latest is 3.0.4. > The package scipion-em is up to date. Your version is 3.0.3 > The package scipion-app is out of date. Your version is 3.0.1, the latest is 3.0.2. > > and then use pip to update? > (.scipion3env) $ pip install scipion-pyworkflow==3.0.4 scipion-app==3.0.2 > > $ scipion3 update > Scipion v3.0.2 () devel > Scipion is up to date. > The package scipion-pyworkflow is up to date. Your version is 3.0.4 > The package scipion-em is up to date. Your version is 3.0.3 > The package scipion-app is up to date. Your version is 3.0.2 > > Cheers, > Wolfgang > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Lugmayr, W. <w.l...@uk...> - 2020-09-28 08:26:54
|
Hi, Is this intended that the update command just prints information? I thought it would update the core packages. $ scipion3 update Scipion v3.0.1 () devel Scipion is up to date. The package scipion-pyworkflow is out of date. Your version is 3.0.3, the latest is 3.0.4. The package scipion-em is up to date. Your version is 3.0.3 The package scipion-app is out of date. Your version is 3.0.1, the latest is 3.0.2. and then use pip to update? (.scipion3env) $ pip install scipion-pyworkflow==3.0.4 scipion-app==3.0.2 $ scipion3 update Scipion v3.0.2 () devel Scipion is up to date. The package scipion-pyworkflow is up to date. Your version is 3.0.4 The package scipion-em is up to date. Your version is 3.0.3 The package scipion-app is up to date. Your version is 3.0.2 Cheers, Wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 22607 Hamburg, Germany Tel.: +49 40 8998-87652 Email: wol...@cs... http://www.cssb-hamburg.de/ |
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From: Pablo C. <pc...@cn...> - 2020-09-18 14:48:20
|
Thanks Dmitry...let us know. On 18/9/20 15:57, Dmitry Semchonok wrote: > > Dear colleagues, > > I suspect the error with Bayesian polishing protocol happened due to > my settings in the relion-motioncor protocol, where I selected to > start the alignment with the second frame/ > > I will re-run the relion-motioncorr with all frames and re-run the > Bayesian polishing again. > > I will report back if that helped. > > Sincerely, > > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Dmitry S. <sem...@gm...> - 2020-09-18 14:04:50
|
<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:612.0pt 792.0pt; margin:2.0cm 42.5pt 2.0cm 3.0cm;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=RU link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Dear colleagues, when I run relion-baesian polishing training protocol I got the following error:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>File 'Runs/031843_ProtRelionBayesianPolishing/logs/run.stdout' doesn't exist00001: RUNNING PROTOCOL -----------------<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00002: HostName: dataanalysisserver1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00003: PID: 7021<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00004: Scipion: v2.0 (2019-04-23) Diocletian<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00005: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00006: workingDir: Runs/031843_ProtRelionBayesianPolishing<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00007: runMode: Continue<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00008: MPI: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00009: threads: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00010: len(steps) 2 len(prevSteps) 0 <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00011: Starting at step: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00012: Running steps <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00013: STARTED: convertInputStep, step 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00014: 2020-09-18 15:43:45.453004<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00015: Converting set from 'Runs/031792_ProtAlignmentAssign/particles.sqlite' into 'Runs/031843_ProtRelionBayesianPolishing/input_particles.star'<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00016: Traceback (most recent call last):<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00017: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, in run<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00018: self._run()<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00019: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, in _run<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00020: resultFiles = self._runFunc()<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00021: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, in _runFunc<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00022: return self._func(*self._args)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00023: File "/usr/local/scipion/software/lib/python2.7/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 242, in convertInputStep<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00024: tableShifts.addRow(i, shiftsX[i-a0] + xoff,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00025: IndexError: list index out of range<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00026: Protocol failed: list index out of range<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00027: FAILED: convertInputStep, step 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00028: 2020-09-18 15:43:45.487204<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00029: *** Last status is failed <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>00030: ------------------- PROTOCOL FAILED (DONE 1/2)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Any ideas how to fix it?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Thank you <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Dmitry<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Dmitry S. <sem...@gm...> - 2020-09-18 13:58:04
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:612.0pt 792.0pt; margin:2.0cm 42.5pt 2.0cm 3.0cm;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=RU link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Dear colleagues,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I suspect the error with Bayesian polishing protocol happened due to my settings in the relion-motioncor protocol, where I selected to start the alignment with the second frame/<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I will re-run the relion-motioncorr with all frames and re-run the Bayesian polishing again.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>I will report back if that helped.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Dmitry<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> </span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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