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From: Hutchison, M. (NIH/N. [C] <hut...@ma...> - 2018-04-25 17:02:51
|
Have you downloaded the appropriate test data set? The test data sets aren't included with the github distribution and are downloaded when you try to run the test (or manually separately from running the test). If your user doesn't have write to scipion/data/tests you'll see this error in the stdout of the import stage as a result of failure to download, which leads to a failure to import the raw data for testing. You should also see a more descriptive error in your terminal that tells you that you have a permissions error (see below for the equivalent when run in a similar scenario on our system). Can you run `/opt/scipion/scipion testdata --list` and confirm that the dataset shows up as a local dataset? If it doesn't, try running `/opt/scipion/scipion testdata --download hemoglobin_mda` (which should be the correct dataset for this test) as a user that can write to scipion/data/tests. Then rerun the relevant test. To answer your last point, the test project and all processing data will be created in $SCIPION_USER_DATA from the config file (by default ~/ScipionUserData), but the raw test dataset writes to the scipion installation directory. My terminal output after replicating this type of failure (the critical issue is the OSError permissions failure): >>>>> python scripts/run_tests.py em.workflows.test_workflow_spiderMDA Running tests.... ('Creating project at: ', '/mnt/nas/Scipion/projects/TestSpiderConvert/project.sqlite') >>>> python /usr/local/scipion/scipion testdata --download hemoglobin_mda /usr/local/scipion/config/scipion.conf /usr/local/scipion/config/scipion.conf Scipion v1.2 (2018-04-02) Caligula >>>>> python scripts/sync_data.py --download hemoglobin_mda Selected datasets: hemoglobin_mda Dataset hemoglobin_mda not in local machine. Downloading... Traceback (most recent call last): File "scripts/sync_data.py", line 440, in <module> main() File "scripts/sync_data.py", line 128, in main download(dataset, url=args.url, verbose=args.verbose) File "scripts/sync_data.py", line 257, in download os.makedirs(datasetFolder) File "/usr/local/scipion/software/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 13] Permission denied: '/usr/local/scipion/data/tests/hemoglobin_mda' ** Running command: 'python /usr/local/scipion/scipion runprotocol pw_protocol_run.py "/mnt/nas/Scipion/projects/TestSpiderConvert" "Runs/000002_ProtImportParticles/logs/run.db" 2' /usr/local/scipion/config/scipion.conf /usr/local/scipion/config/scipion.conf Scipion v1.2 (2018-04-02) Caligula >>>>> python /usr/local/scipion/pyworkflow/apps/pw_protocol_run.py "/mnt/nas/Scipion/projects/TestSpiderConvert" "Runs/000002_ProtImportParticles/logs/run.db" "2" >>> ERROR running protocol scipion - import particles [ FAILED ] TestSpiderConvert.test_convert Traceback (most recent call last): File "/usr/local/scipion/software/lib/python2.7/unittest/case.py", line 329, in run testMethod() File "/usr/local/scipion/pyworkflow/tests/em/workflows/test_workflow_spiderMDA.py", line 52, in test_convert self.launchProtocol(protImport) File "/usr/local/scipion/pyworkflow/tests/tests.py", line 106, in launchProtocol raise Exception("ERROR: Protocol not finished") Exception: ERROR: Protocol not finished ('Creating project at: ', '/mnt/nas/Scipion/projects/TestSpiderWorkflow/project.sqlite') >>>> python /usr/local/scipion/scipion testdata --download hemoglobin_mda /usr/local/scipion/config/scipion.conf /usr/local/scipion/config/scipion.conf Scipion v1.2 (2018-04-02) Caligula >>>>> python scripts/sync_data.py --download hemoglobin_mda Selected datasets: hemoglobin_mda Dataset hemoglobin_mda not in local machine. Downloading... Traceback (most recent call last): File "scripts/sync_data.py", line 440, in <module> main() File "scripts/sync_data.py", line 128, in main download(dataset, url=args.url, verbose=args.verbose) File "scripts/sync_data.py", line 257, in download os.makedirs(datasetFolder) File "/usr/local/scipion/software/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 13] Permission denied: '/usr/local/scipion/data/tests/hemoglobin_mda' ** Running command: 'python /usr/local/scipion/scipion runprotocol pw_protocol_run.py "/mnt/nas/Scipion/projects/TestSpiderWorkflow" "Runs/000002_ProtImportParticles/logs/run.db" 2' /usr/local/scipion/config/scipion.conf /usr/local/scipion/config/scipion.conf Scipion v1.2 (2018-04-02) Caligula >>>>> python /usr/local/scipion/pyworkflow/apps/pw_protocol_run.py "/mnt/nas/Scipion/projects/TestSpiderWorkflow" "Runs/000002_ProtImportParticles/logs/run.db" "2" >>> ERROR running protocol scipion - import particles [ FAILED ] TestSpiderWorkflow.test_mdaWorkflow Traceback (most recent call last): File "/usr/local/scipion/software/lib/python2.7/unittest/case.py", line 329, in run testMethod() File "/usr/local/scipion/pyworkflow/tests/em/workflows/test_workflow_spiderMDA.py", line 96, in test_mdaWorkflow self.launchProtocol(protImport) File "/usr/local/scipion/pyworkflow/tests/tests.py", line 106, in launchProtocol raise Exception("ERROR: Protocol not finished") Exception: ERROR: Protocol not finished [==========] run 2 tests (2.991 secs) [ FAILED ] 2 tests [ PASSED ] 0 tests On 4/25/18, 12:38 PM, "Patrick Goetz" <pg...@ma...> wrote: Hi - Sorry for continuously spamming the list, but the Spider MDA Workflow test isn't working again, I just want to make sure I haven't introduced structural installation problems. First, I re-installed Scipion in /opt so that the users can access it, and made sure to install the spider package. Now running scipion as an ordinary user: /opt/scipion/scipion tests em.workflows.test_workflow_spiderMDA I get error messages and "2 Tests failed" again. Snooping around in the locally created ScipionUserData folder, I found this note in ~/ScipionUserData/projects/TestSpiderWorkflow/Runs/000002_ProtImportParticles/logs/run.stdout: ------- Traceback (most recent call last): File "/opt/scipion/pyworkflow/protocol/protocol.py", line 186, in run self._run() File "/opt/scipion/pyworkflow/protocol/protocol.py", line 1104, in _run 'Protocol.run: Validation errors:\n' + '\n'.join(errors)) Exception: Protocol.run: Validation errors: There are no files matching the pattern /opt/scipion/data/tests/hemoglobin_mda/particles/*.spi ------- So apparently the test is trying to install data to /opt/scipion/data rather than ~/ScipionUserData ? Am I missing a configuration step that would instruct the system to process all data in the user's ScipionUserData folder? ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
From: Patrick G. <pg...@ma...> - 2018-04-25 16:37:35
|
Hi - Sorry for continuously spamming the list, but the Spider MDA Workflow test isn't working again, I just want to make sure I haven't introduced structural installation problems. First, I re-installed Scipion in /opt so that the users can access it, and made sure to install the spider package. Now running scipion as an ordinary user: /opt/scipion/scipion tests em.workflows.test_workflow_spiderMDA I get error messages and "2 Tests failed" again. Snooping around in the locally created ScipionUserData folder, I found this note in ~/ScipionUserData/projects/TestSpiderWorkflow/Runs/000002_ProtImportParticles/logs/run.stdout: ------- Traceback (most recent call last): File "/opt/scipion/pyworkflow/protocol/protocol.py", line 186, in run self._run() File "/opt/scipion/pyworkflow/protocol/protocol.py", line 1104, in _run 'Protocol.run: Validation errors:\n' + '\n'.join(errors)) Exception: Protocol.run: Validation errors: There are no files matching the pattern /opt/scipion/data/tests/hemoglobin_mda/particles/*.spi ------- So apparently the test is trying to install data to /opt/scipion/data rather than ~/ScipionUserData ? Am I missing a configuration step that would instruct the system to process all data in the user's ScipionUserData folder? |
From: Patrick G. <pg...@ma...> - 2018-04-25 14:20:12
|
Hi Kyle On 04/25/2018 01:31 AM, Kyle Douglass wrote: > verify that spider_linux_mp_intel64 exists and has execute permissions > set? You can use the command > > ls -l /root/scipion/software/em/spider-21.13/spider/bin/ | grep > spider_linux_mp_intel64 > This was the problem. I didn't notice that the spider package needs to be installed separately even though it's right there in the documentation. Now the test works as advertised. Thanks for your help with this. |
From: Jose M. de la R. T. <del...@gm...> - 2018-04-25 14:18:33
|
ScipionUserData is a folder independent from the scipion installation folder and each user has its own ScipionUserData...by default it goes to ~/ScipionUserData. On Wed, Apr 25, 2018 at 4:15 PM, Patrick Goetz <pg...@ma...> wrote: > On 04/25/2018 09:06 AM, Jose Miguel de la Rosa Trevin wrote: > >> The users only need read/execution permissions and a way to find the >> scipion script inside the installation folder. >> >> > What about the ScipionUserData folder -- does this just need to be located > in parallel to scipion, or is there a way I can put scipion into /opt and > ScipionUserData in /var or /home/per_user? And presumably users would need > permission to write to this folder? > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
From: Patrick G. <pg...@ma...> - 2018-04-25 14:16:04
|
On 04/25/2018 09:06 AM, Jose Miguel de la Rosa Trevin wrote: > The users only need read/execution permissions and a way to find the > scipion script inside the installation folder. > What about the ScipionUserData folder -- does this just need to be located in parallel to scipion, or is there a way I can put scipion into /opt and ScipionUserData in /var or /home/per_user? And presumably users would need permission to write to this folder? |
From: Jose M. de la R. T. <del...@gm...> - 2018-04-25 14:06:44
|
The users only need read/execution permissions and a way to find the scipion script inside the installation folder. On Wed, Apr 25, 2018 at 3:48 PM, Patrick Goetz <pg...@ma...> wrote: > > On 04/25/2018 02:07 AM, Jose Miguel de la Rosa Trevin wrote: > >> We have designed scipion to avoid modifying you environment...so, user >> only need to point to the scipion python script from the installation >> folder. Two possibilities are: >> a) Define an alias to that: alias scipion='/path/to/scipion/scipion' >> b) Add the /path/to/scipion to the user PATH environment variable >> All the environment settings for each process are done on the fly, this >> means that will not interfere between packages or with the system libraries. >> >> > That's very nice, actually. So all I need to do is move the Scipion > folder to a publicly accessible location (e.g. /opt/scipion or > /usr/local/scipion), make sure the users can find the scipion command, and > make sure that the read/write/execute permissions are properly set? > > > > > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
From: Patrick G. <pg...@ma...> - 2018-04-25 13:48:30
|
On 04/25/2018 02:07 AM, Jose Miguel de la Rosa Trevin wrote: > We have designed scipion to avoid modifying you environment...so, user > only need to point to the scipion python script from the installation > folder. Two possibilities are: > a) Define an alias to that: alias scipion='/path/to/scipion/scipion' > b) Add the /path/to/scipion to the user PATH environment variable > All the environment settings for each process are done on the fly, this > means that will not interfere between packages or with the system > libraries. > That's very nice, actually. So all I need to do is move the Scipion folder to a publicly accessible location (e.g. /opt/scipion or /usr/local/scipion), make sure the users can find the scipion command, and make sure that the read/write/execute permissions are properly set? |
From: Jose M. de la R. T. <del...@gm...> - 2018-04-25 07:07:47
|
Hi Patrick, Find some clarification below, on top of the suggestions from Kyle. On Tue, Apr 24, 2018 at 11:21 PM, Patrick Goetz <pg...@ma...> wrote: > Hi - > > I've managed to install Scipion (with --no-opencv) on Ubuntu 18.04. > > Missing from the instructions is the need for this package: > libreadline-dev > > The readline.h header file is needed for the sqlite compilation. > > Also, the file ~/scipion/config/scipion.conf required several > modifications to MPI, CUDA, and Matlab paths. > > I also installed EMAN2 using: ./scipion install --no-xmipp eman-2.12 > > Now unfortunately I have a number of questions. > > 1. > I cloned the git repo into /root, and now everything is installed under > > /root/scipion > > How should I make the software available to users? It seems that source > and binaries are heavily intertwined here. The scipion command is in > /root/scipion, but everything else is installed in /root/scipion/software? > > Presumably this also means setting some environment variables (at least a > path)? > It is true that source and binaries are intertwined now, we want to improve this in the future. We have designed scipion to avoid modifying you environment...so, user only need to point to the scipion python script from the installation folder. Two possibilities are: a) Define an alias to that: alias scipion='/path/to/scipion/scipion' b) Add the /path/to/scipion to the user PATH environment variable All the environment settings for each process are done on the fly, this means that will not interfere between packages or with the system libraries. > > 2. > I tried running one of the small tests (scipion tests > em.workflows.test_workflow_spiderMDA), but this failed with a couple of > python runtime errors. These look like internal errors, but could this > have something to do with the fact that I'm trying to run the test from a > (non-graphical) terminal as root (because of the install location)? > > As Kyle pointed out, the error is a missing binary file. My guess would be that you haven't installed spider (scipion install spider --no-xmipp) and you are trying to run a test that use it. The test data sets are written in /path/to/scipion/data/tests, so, if this folder belong to root, you will need to run the tests with root or give user access. Additionally, the projects that are generated by each test go to the same data folder of each user (~/ScipionUserData by default) Hope this helps Best, Jose Miguel > > Fetching files of dataset "hemoglobin_mda"... > ################################################# > ** Running command: 'python /root/scipion/scipion runprotocol > pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderConvert" > "Runs/000002_ProtImportParticles/logs/run.db" 2' > > Scipion v1.2 (2018-04-02) Caligula > > >>>>> python /root/scipion/pyworkflow/apps/pw_protocol_run.py > "/root/ScipionUserData/projects/TestSpiderConvert" > "Runs/000002_ProtImportParticles/logs/run.db" "2" > stackFn: /root/ScipionUserData/projects/TestSpiderConvert/stack.stk > ** Running command: /root/scipion/software/em/spid > er-21.13/spider/bin/spider_linux_mp_intel64 stk @cp_endian > /bin/sh: 1: /root/scipion/software/em/spider-21.13/spider/bin/spider_linux_mp_intel64: > not found > [ FAILED ] TestSpiderConvert.test_convert > > Traceback (most recent call last): > File "/root/scipion/software/lib/python2.7/unittest/case.py", line 329, > in run > testMethod() > File "/root/scipion/pyworkflow/tests/em/workflows/test_workflow_spiderMDA.py", > line 62, in test_convert > writeSetOfImages(protImport.outputParticles, stackFn, selFn) > File "/root/scipion/pyworkflow/em/packages/spider/convert.py", line 86, > in writeSetOfImages > convertEndian(stackFn, imgSet.getSize()) > File "/root/scipion/pyworkflow/em/packages/spider/convert.py", line > 103, in convertEndian > }, cwd=fnDir) > File "/root/scipion/pyworkflow/em/packages/spider/spider.py", line 177, > in runTemplate > runScript(outputScript, ext, log, cwd) > File "/root/scipion/pyworkflow/em/packages/spider/spider.py", line 183, > in runScript > runJob(log, SPIDER, args, env=dict(environment), cwd=cwd) > File "/root/scipion/pyworkflow/utils/process.py", line 51, in runJob > return runCommand(command, env, cwd) > File "/root/scipion/pyworkflow/utils/process.py", line 65, in runCommand > check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, > env=env, cwd=cwd) > File "/root/scipion/software/lib/python2.7/subprocess.py", line 186, in > check_call > raise CalledProcessError(retcode, cmd) > CalledProcessError: Command '/root/scipion/software/em/spi > der-21.13/spider/bin/spider_linux_mp_intel64 stk @cp_endian' returned > non-zero exit status 127 > ('Creating project at: ', '/root/ScipionUserData/project > s/TestSpiderWorkflow/project.sqlite') > >>>> python /root/scipion/scipion testdata --download hemoglobin_mda > > Scipion v1.2 (2018-04-02) Caligula > > >>>>> python scripts/sync_data.py --download hemoglobin_mda > Selected datasets: hemoglobin_mda > Local copy of dataset hemoglobin_mda detected. > Checking for updates... > Regenerating local MANIFEST... > Verifying MD5s... > ...done. Updated files: 0 > ** Running command: 'python /root/scipion/scipion runprotocol > pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderWorkflow" > "Runs/000002_ProtImportParticles/logs/run.db" 2' > > Scipion v1.2 (2018-04-02) Caligula > > >>>>> python /root/scipion/pyworkflow/apps/pw_protocol_run.py > "/root/ScipionUserData/projects/TestSpiderWorkflow" > "Runs/000002_ProtImportParticles/logs/run.db" "2" > ** Running command: 'python /root/scipion/scipion runprotocol > pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderWorkflow" > "Runs/000070_SpiderProtFilter/logs/run.db" 70' > > Scipion v1.2 (2018-04-02) Caligula > > >>>>> python /root/scipion/pyworkflow/apps/pw_protocol_run.py > "/root/ScipionUserData/projects/TestSpiderWorkflow" > "Runs/000070_SpiderProtFilter/logs/run.db" "70" > > >>> ERROR running protocol scipion - filter particles > [ FAILED ] TestSpiderWorkflow.test_mdaWorkflow > > Traceback (most recent call last): > File "/root/scipion/software/lib/python2.7/unittest/case.py", line 329, > in run > testMethod() > File "/root/scipion/pyworkflow/tests/em/workflows/test_workflow_spiderMDA.py", > line 104, in test_mdaWorkflow > self.launchProtocol(protFilter) > File "/root/scipion/pyworkflow/tests/tests.py", line 106, in > launchProtocol > raise Exception("ERROR: Protocol not finished") > Exception: ERROR: Protocol not finished > > [==========] run 2 tests (46.593 secs) > [ FAILED ] 2 tests > [ PASSED ] 0 tests > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
From: Kyle D. <kyl...@ep...> - 2018-04-25 06:32:07
|
Hi Patrick, (I'm not a Scipion dev but have some suggestions.) On 04/24/2018 11:21 PM, Patrick Goetz wrote: > > > 2. > I tried running one of the small tests (scipion tests > em.workflows.test_workflow_spiderMDA), but this failed with a couple > of python runtime errors. These look like internal errors, but could > this have something to do with the fact that I'm trying to run the > test from a (non-graphical) terminal as root (because of the install > location)? > > > File "/root/scipion/software/lib/python2.7/subprocess.py", line 186, > in check_call > raise CalledProcessError(retcode, cmd) > CalledProcessError: Command > '/root/scipion/software/em/spider-21.13/spider/bin/spider_linux_mp_intel64 > stk @cp_endian' returned non-zero exit status 127 > ('Creating project at: ', > '/root/ScipionUserData/projects/TestSpiderWorkflow/project.sqlite') > >>>> python /root/scipion/scipion testdata --download hemoglobin_mda > > Actually it looks like that error is coming from a call to a system command and is not directly caused by anything in Python. Exit status 127 is returned when either 1) the file does not exist or 2) the file does not have execute permission for your user or group. Could you verify that spider_linux_mp_intel64 exists and has execute permissions set? You can use the command ls -l /root/scipion/software/em/spider-21.13/spider/bin/ | grep spider_linux_mp_intel64 and check that an 'x' exists for the user/group? (I assume it's the root user.) I would also think that you should give everyone read/write access to the ScipionUserData folder since you want multiple users to have access to it; this may not be true in your case since it is buried inside a folder belonging to root. Finally, there are log files for stdout and stderr that are written to the ScipionUserData folder when you run a workflow or test. In my experience you can get more information about any errors from these files. Hope this helps, Kyle -- Kyle M. Douglass, PhD Post-doctoral researcher The Laboratory of Experimental Biophysics EPFL, Lausanne, Switzerland http://kmdouglass.github.io http://leb.epfl.ch |
From: Patrick G. <pg...@ma...> - 2018-04-24 21:56:20
|
Hi - I've managed to install Scipion (with --no-opencv) on Ubuntu 18.04. Missing from the instructions is the need for this package: libreadline-dev The readline.h header file is needed for the sqlite compilation. Also, the file ~/scipion/config/scipion.conf required several modifications to MPI, CUDA, and Matlab paths. I also installed EMAN2 using: ./scipion install --no-xmipp eman-2.12 Now unfortunately I have a number of questions. 1. I cloned the git repo into /root, and now everything is installed under /root/scipion How should I make the software available to users? It seems that source and binaries are heavily intertwined here. The scipion command is in /root/scipion, but everything else is installed in /root/scipion/software? Presumably this also means setting some environment variables (at least a path)? 2. I tried running one of the small tests (scipion tests em.workflows.test_workflow_spiderMDA), but this failed with a couple of python runtime errors. These look like internal errors, but could this have something to do with the fact that I'm trying to run the test from a (non-graphical) terminal as root (because of the install location)? Fetching files of dataset "hemoglobin_mda"... ################################################# ** Running command: 'python /root/scipion/scipion runprotocol pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderConvert" "Runs/000002_ProtImportParticles/logs/run.db" 2' Scipion v1.2 (2018-04-02) Caligula >>>>> python /root/scipion/pyworkflow/apps/pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderConvert" "Runs/000002_ProtImportParticles/logs/run.db" "2" stackFn: /root/ScipionUserData/projects/TestSpiderConvert/stack.stk ** Running command: /root/scipion/software/em/spider-21.13/spider/bin/spider_linux_mp_intel64 stk @cp_endian /bin/sh: 1: /root/scipion/software/em/spider-21.13/spider/bin/spider_linux_mp_intel64: not found [ FAILED ] TestSpiderConvert.test_convert Traceback (most recent call last): File "/root/scipion/software/lib/python2.7/unittest/case.py", line 329, in run testMethod() File "/root/scipion/pyworkflow/tests/em/workflows/test_workflow_spiderMDA.py", line 62, in test_convert writeSetOfImages(protImport.outputParticles, stackFn, selFn) File "/root/scipion/pyworkflow/em/packages/spider/convert.py", line 86, in writeSetOfImages convertEndian(stackFn, imgSet.getSize()) File "/root/scipion/pyworkflow/em/packages/spider/convert.py", line 103, in convertEndian }, cwd=fnDir) File "/root/scipion/pyworkflow/em/packages/spider/spider.py", line 177, in runTemplate runScript(outputScript, ext, log, cwd) File "/root/scipion/pyworkflow/em/packages/spider/spider.py", line 183, in runScript runJob(log, SPIDER, args, env=dict(environment), cwd=cwd) File "/root/scipion/pyworkflow/utils/process.py", line 51, in runJob return runCommand(command, env, cwd) File "/root/scipion/pyworkflow/utils/process.py", line 65, in runCommand check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, env=env, cwd=cwd) File "/root/scipion/software/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command '/root/scipion/software/em/spider-21.13/spider/bin/spider_linux_mp_intel64 stk @cp_endian' returned non-zero exit status 127 ('Creating project at: ', '/root/ScipionUserData/projects/TestSpiderWorkflow/project.sqlite') >>>> python /root/scipion/scipion testdata --download hemoglobin_mda Scipion v1.2 (2018-04-02) Caligula >>>>> python scripts/sync_data.py --download hemoglobin_mda Selected datasets: hemoglobin_mda Local copy of dataset hemoglobin_mda detected. Checking for updates... Regenerating local MANIFEST... Verifying MD5s... ...done. Updated files: 0 ** Running command: 'python /root/scipion/scipion runprotocol pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderWorkflow" "Runs/000002_ProtImportParticles/logs/run.db" 2' Scipion v1.2 (2018-04-02) Caligula >>>>> python /root/scipion/pyworkflow/apps/pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderWorkflow" "Runs/000002_ProtImportParticles/logs/run.db" "2" ** Running command: 'python /root/scipion/scipion runprotocol pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderWorkflow" "Runs/000070_SpiderProtFilter/logs/run.db" 70' Scipion v1.2 (2018-04-02) Caligula >>>>> python /root/scipion/pyworkflow/apps/pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderWorkflow" "Runs/000070_SpiderProtFilter/logs/run.db" "70" >>> ERROR running protocol scipion - filter particles [ FAILED ] TestSpiderWorkflow.test_mdaWorkflow Traceback (most recent call last): File "/root/scipion/software/lib/python2.7/unittest/case.py", line 329, in run testMethod() File "/root/scipion/pyworkflow/tests/em/workflows/test_workflow_spiderMDA.py", line 104, in test_mdaWorkflow self.launchProtocol(protFilter) File "/root/scipion/pyworkflow/tests/tests.py", line 106, in launchProtocol raise Exception("ERROR: Protocol not finished") Exception: ERROR: Protocol not finished [==========] run 2 tests (46.593 secs) [ FAILED ] 2 tests [ PASSED ] 0 tests |
From: Pablo C. <pc...@cn...> - 2018-04-20 12:47:25
|
Hi Patrick, to be honest , I don't know how libreadline6 is used,,, I would say that since it is not _dev we don't need it at compile time but at runtime But I might be wrong. Try dev_7 ? Will it work? On 19/04/18 15:59, Patrick Goetz wrote: > Hi Pablo - > > Thanks very much for your help with this. I will try the config > suggestions you provided; meanwhile, regarding libreadline6: > > > On 04/19/2018 12:49 AM, Pablo Conesa wrote: >> To me, it seems that libreadline6 hasn't made it to bionic, yet?: >> > > > My bad; I should have checked the Xenial (16.04) package list first. > However, it doesn't look like libreadline6 is going to make it into > Bionic (18.04). Here is the related package list obtained by > searching the package directories on packages.ubuntu.com for > "libreadline": > > Package libreadline-dev [this is version 7] > > Package libreadline5 > > Package libreadline5-dbg > > Package libreadline6-dev > > Package libreadline7 > > Package libreadline7-dbg > > > Looks like they went to version 7, while retaining version 5, but not > 6. Is this a compile time or a run time dependency? If compile time, > one would usually need the -dev version anyway. > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
From: Patrick G. <pg...@ma...> - 2018-04-19 14:34:07
|
Hi Pablo - Thanks very much for your help with this. I will try the config suggestions you provided; meanwhile, regarding libreadline6: On 04/19/2018 12:49 AM, Pablo Conesa wrote: > To me, it seems that libreadline6 hasn't made it to bionic, yet?: > My bad; I should have checked the Xenial (16.04) package list first. However, it doesn't look like libreadline6 is going to make it into Bionic (18.04). Here is the related package list obtained by searching the package directories on packages.ubuntu.com for "libreadline": Package libreadline-dev [this is version 7] Package libreadline5 Package libreadline5-dbg Package libreadline6-dev Package libreadline7 Package libreadline7-dbg Looks like they went to version 7, while retaining version 5, but not 6. Is this a compile time or a run time dependency? If compile time, one would usually need the -dev version anyway. |
From: Pablo C. <pc...@cn...> - 2018-04-19 05:50:07
|
Hi Patrick, We have default values for the paths of several dependencies, like MPI or JAVA. Our current default values do not match Ubuntu paths. At this point you can: 1.- run: ./scipion config --overwrite This tries to guess those paths, and in Ubuntu 14 --> 16 works fine. Sorry never tried on ubuntu 18! 2.- Manually, edit the config file: this file can be found at <SCIPION_HOME>/config/scipion.conf Regarding the libreadline6,....could this be a change related to ubuntu 18? To me, it seems that libreadline6 hasn't made it to bionic, yet?: <https://packages.ubuntu.com/trusty/libreadline6,%20yet> Whereas, the dev version has made it! <https://packages.ubuntu.com/trusty/libreadline6-dev> I have added a note in our wiki!! Thanks for the feedback! Patrick, probably you are the first one to install Scipion in Ubuntu 18. Please let us know how it goes, whether if it goes right and more importantly if something does wrong. All the best, Pablo. On 18/04/18 19:40, Patrick Goetz wrote: > Hi - > > I'm trying to configure Scipion cloned from the git repo on an Ubuntu > 18.04 machine and get the following error message: > > ----------------- > Checking paths in /root/scipion/config/scipion.conf ... > Path to MPI_LIBDIR (/usr/lib64/mpi/gcc/openmpi/lib) should exist but > it doesn't. > Path to MPI_INCLUDE (/usr/lib64/mpi/gcc/openmpi/include) should > exist but it doesn't. > Cannot find file: /usr/lib64/mpi/gcc/openmpi/include/mpi.h > Errors found. > ----------------- > > I think it's looking for the MPI header file in the wrong location for > Ubuntu? It's here: > > /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h > > > Also, minor point. The installation instructions have a list of > dependencies that need to be installed which includes "libreadline6". > There's no installation candidate for this, I think it needs to be > lib64readline6-dev instead. > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
From: Patrick G. <pg...@ma...> - 2018-04-18 18:14:14
|
Hi - I'm trying to configure Scipion cloned from the git repo on an Ubuntu 18.04 machine and get the following error message: ----------------- Checking paths in /root/scipion/config/scipion.conf ... Path to MPI_LIBDIR (/usr/lib64/mpi/gcc/openmpi/lib) should exist but it doesn't. Path to MPI_INCLUDE (/usr/lib64/mpi/gcc/openmpi/include) should exist but it doesn't. Cannot find file: /usr/lib64/mpi/gcc/openmpi/include/mpi.h Errors found. ----------------- I think it's looking for the MPI header file in the wrong location for Ubuntu? It's here: /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h Also, minor point. The installation instructions have a list of dependencies that need to be installed which includes "libreadline6". There's no installation candidate for this, I think it needs to be lib64readline6-dev instead. |
From: Laura d. C. <su...@bc...> - 2018-04-18 12:11:26
|
Hi Abhisek, did you install Relion through Scipion or you had it before? You should also make sure MPI variables at SCIPION_HOME/config/scipion.conf are correctly set (I guess they are, otherwise you would have seen some complaint when running scipion config). These are my variables on an Ubuntu16 using openmpi. MPI_CC = mpicc MPI_CXX = mpiCC MPI_LINKERFORPROGRAMS = mpiCC MPI_LIB = mpi MPI_LIBDIR = /usr/lib/openmpi/lib MPI_INCLUDE = /usr/lib/openmpi/include MPI_BINDIR = /usr/bin best regards Laura Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/316 Activo Sab, 7 Abril at 8:27 AM , Mailing list for Scipion users <sci...@li...> Escrito: Hi, My Relion-2.1 in scipion keep raising this error: [localhost.localdomain:05066] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005 00036: *** An error occurred in MPI_Init 00037: *** on a NULL communicator 00038: *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, 00039: *** and potentially your MPI job) 00040: [localhost.localdomain:5066] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! What is surprising to me is Xmipp3-cl2d is running alright in MPI but Relion-2D classification is getting crashed. Please help me out here. thank you -- Abhisek Mondal Senior Research Fellow Structural Biology and Bioinformatics Division CSIR-Indian Institute of Chemical Biology Kolkata 700032 INDIA |
From: Jonathan R. <jon...@no...> - 2018-04-14 15:47:45
|
Thank you all for your help. We have just installed the development version (1.2) and it shows the phase shifts just as you say. This is a very helpful interface you have built. Best wishes, Jonathan On Sat, Apr 14, 2018, 3:57 AM Carlos Oscar Sorzano <co...@cn...> wrote: > Thank you, Gregory, for the clarification. > > On 14/04/2018 10:46, Gregory Sharov wrote: > > Hello, Jonathan > > As Pablo mentioned earlier, phase shift from gctf was incorrectly parsed > in many cases from output files in version 1.1, in 1.2 this should be > fixed now. Carlos is referring to phase shift calculation by xmipp, which > is not available yet. > > On Sat, Apr 14, 2018, 09:18 Carlos Oscar Sorzano <co...@cn...> wrote: > >> Dear Jonathan, >> >> phase shift was not calculated in v1.1, it has been added in the >> development branch, and it will be present in next release. >> >> Kind regards, Carlos Oscar >> >> On 13/04/2018 0:59, Jonathan Remis wrote: >> >> >> Hello, >> >> I am using SCIPION v1.1 and want to use a streaming data pipeline to give >> me a live readout of phase shifts as I collect images using gctf. Unlike >> most of the other information determined in the CTF estimation I don't see >> any columns for phase shift. I do see the values in >> >> */Runs/xxx_ProtGctf/extra/micrograph_name/ctfEstimation.txt * >> >> Perhaps there is a way to extract this data from the file but the format >> of the file doesn't allow me to grep it, or at least I don't know how to do >> this. >> >> If I am overlooking something or if you know of a way I could more easily >> get this information it would be quite useful. >> >> >> Thanks for your help< >> Jonathan >> >> >> -- >> >> ------------------------------ >> >> *JONATHAN REMIS* >> >> CryoEM Facilities Manager >> >> >> Northwestern University >> >> Department of Molecular Biosciences >> >> >> mailing address >> >> 2205 Tech Drive >> >> Hogan 2-100 >> >> Evanston, IL 60208-3500 >> >> USA >> >> >> *OFFICE* +1-847-491-7813 >> >> *EMAIL * jon...@no... <jon...@ab...> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> >> >> >> >> _______________________________________________ >> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> >> >> >> -- >> ------------------------------------------------------------------------ >> Carlos Oscar Sánchez Sorzano e-mail: co...@cn... >> Biocomputing unit http://i2pc.es/coss <https://urldefense.proofpoint.com/v2/url?u=http-3A__i2pc.es_coss&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=ttaI9AfvlwszvKSNNMKdJFsXZNd6ygBzf4-kSgcF6Bw&e=> >> National Center of Biotechnology (CSIC) >> c/Darwin, 3 >> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> >> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> > > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail: co...@cn... > Biocomputing unit http://i2pc.es/coss <https://urldefense.proofpoint.com/v2/url?u=http-3A__i2pc.es_coss&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=ttaI9AfvlwszvKSNNMKdJFsXZNd6ygBzf4-kSgcF6Bw&e=> > National Center of Biotechnology (CSIC) > c/Darwin, 3 > Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 > 28049 MADRID (SPAIN) Fax: 34-91-585 4506 > ------------------------------------------------------------------------ > > |
From: Jonathan R. <re...@gm...> - 2018-04-14 14:15:31
|
Thank you all for your help. We have just installed the development version (1.2) and it shows the phase shifts just as you say. This is a very helpful interface you have built. Best wishes, Jonathan On Sat, Apr 14, 2018 at 3:57 AM, Carlos Oscar Sorzano <co...@cn...> wrote: > Thank you, Gregory, for the clarification. > > On 14/04/2018 10:46, Gregory Sharov wrote: > > Hello, Jonathan > > As Pablo mentioned earlier, phase shift from gctf was incorrectly parsed > in many cases from output files in version 1.1, in 1.2 this should be > fixed now. Carlos is referring to phase shift calculation by xmipp, which > is not available yet. > > On Sat, Apr 14, 2018, 09:18 Carlos Oscar Sorzano <co...@cn...> wrote: > >> Dear Jonathan, >> >> phase shift was not calculated in v1.1, it has been added in the >> development branch, and it will be present in next release. >> >> Kind regards, Carlos Oscar >> >> On 13/04/2018 0:59, Jonathan Remis wrote: >> >> >> Hello, >> >> I am using SCIPION v1.1 and want to use a streaming data pipeline to give >> me a live readout of phase shifts as I collect images using gctf. Unlike >> most of the other information determined in the CTF estimation I don't see >> any columns for phase shift. I do see the values in >> >> */Runs/xxx_ProtGctf/extra/micrograph_name/ctfEstimation.txt * >> >> Perhaps there is a way to extract this data from the file but the format >> of the file doesn't allow me to grep it, or at least I don't know how to do >> this. >> >> If I am overlooking something or if you know of a way I could more easily >> get this information it would be quite useful. >> >> >> Thanks for your help< >> Jonathan >> >> >> -- >> >> ------------------------------ >> >> *JONATHAN REMIS* >> >> CryoEM Facilities Manager >> >> >> Northwestern University >> >> Department of Molecular Biosciences >> >> >> mailing address >> >> 2205 Tech Drive >> >> Hogan 2-100 >> >> Evanston, IL 60208-3500 >> >> USA >> >> >> *OFFICE* +1-847-491-7813 >> >> *EMAIL * jon...@no... <jon...@ab...> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> >> >> >> >> _______________________________________________ >> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> >> >> >> -- >> ------------------------------------------------------------------------ >> Carlos Oscar Sánchez Sorzano e-mail: co...@cn... >> Biocomputing unit http://i2pc.es/coss <https://urldefense.proofpoint.com/v2/url?u=http-3A__i2pc.es_coss&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=ttaI9AfvlwszvKSNNMKdJFsXZNd6ygBzf4-kSgcF6Bw&e=> >> National Center of Biotechnology (CSIC) >> c/Darwin, 3 >> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> >> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> > > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail: co...@cn... > Biocomputing unit http://i2pc.es/coss <https://urldefense.proofpoint.com/v2/url?u=http-3A__i2pc.es_coss&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=ttaI9AfvlwszvKSNNMKdJFsXZNd6ygBzf4-kSgcF6Bw&e=> > National Center of Biotechnology (CSIC) > c/Darwin, 3 > Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 > 28049 MADRID (SPAIN) Fax: 34-91-585 4506 > ------------------------------------------------------------------------ > > |
From: Carlos O. S. <co...@cn...> - 2018-04-14 08:57:40
|
Thank you, Gregory, for the clarification. On 14/04/2018 10:46, Gregory Sharov wrote: > Hello, Jonathan > > As Pablo mentioned earlier, phase shift from gctf was incorrectly > parsed in many cases from output files in version 1.1, in 1.2 this > should be fixed now. Carlos is referring to phase shift calculation by > xmipp, which is not available yet. > > On Sat, Apr 14, 2018, 09:18 Carlos Oscar Sorzano <co...@cn... > <mailto:co...@cn...>> wrote: > > Dear Jonathan, > > phase shift was not calculated in v1.1, it has been added in the > development branch, and it will be present in next release. > > Kind regards, Carlos Oscar > > > On 13/04/2018 0:59, Jonathan Remis wrote: >> >> Hello, >> >> I am using SCIPION v1.1 and want to use a streaming data pipeline >> to give me a live readout of phase shifts as I collect images >> using gctf. Unlike most of the other information determined in >> the CTF estimation I don't see any columns for phase shift. I do >> see the values in >> >> //Runs/xxx_ProtGctf/extra/micrograph_name/ctfEstimation.txt / >> / >> / >> Perhaps there is a way to extract this data from the file but the >> format of the file doesn't allow me to grep it, or at least I >> don't know how to do this. >> >> If I am overlooking something or if you know of a way I could >> more easily get this information it would be quite useful. >> >> >> Thanks for your help< >> Jonathan >> >> >> -- >> >> ------------------------------------------------------------------------ >> >> *JONATHAN REMIS* >> >> CryoEM Facilities Manager >> >> >> Northwestern University >> >> Department of Molecular Biosciences >> >> >> mailing address >> >> 2205 Tech Drive >> >> Hogan 2-100 >> >> Evanston, IL 60208-3500 >> >> USA >> >> >> *OFFICE*+1-847-491-7813 >> >> *EMAIL *jon...@no... >> <mailto:jon...@ab...> >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail:co...@cn... <mailto:co...@cn...> > Biocomputing unithttp://i2pc.es/coss > National Center of Biotechnology (CSIC) > c/Darwin, 3 > Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 > 28049 MADRID (SPAIN) Fax: 34-91-585 4506 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! > http://sdm.link/slashdot_______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://i2pc.es/coss National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
From: Gregory S. <sha...@gm...> - 2018-04-14 08:46:40
|
Hello, Jonathan As Pablo mentioned earlier, phase shift from gctf was incorrectly parsed in many cases from output files in version 1.1, in 1.2 this should be fixed now. Carlos is referring to phase shift calculation by xmipp, which is not available yet. On Sat, Apr 14, 2018, 09:18 Carlos Oscar Sorzano <co...@cn...> wrote: > Dear Jonathan, > > phase shift was not calculated in v1.1, it has been added in the > development branch, and it will be present in next release. > > Kind regards, Carlos Oscar > > On 13/04/2018 0:59, Jonathan Remis wrote: > > > Hello, > > I am using SCIPION v1.1 and want to use a streaming data pipeline to give > me a live readout of phase shifts as I collect images using gctf. Unlike > most of the other information determined in the CTF estimation I don't see > any columns for phase shift. I do see the values in > > */Runs/xxx_ProtGctf/extra/micrograph_name/ctfEstimation.txt * > > Perhaps there is a way to extract this data from the file but the format > of the file doesn't allow me to grep it, or at least I don't know how to do > this. > > If I am overlooking something or if you know of a way I could more easily > get this information it would be quite useful. > > > Thanks for your help< > Jonathan > > > -- > > ------------------------------ > > *JONATHAN REMIS* > > CryoEM Facilities Manager > > > Northwestern University > > Department of Molecular Biosciences > > > mailing address > > 2205 Tech Drive > > Hogan 2-100 > > Evanston, IL 60208-3500 > > USA > > > *OFFICE* +1-847-491-7813 > > *EMAIL * jon...@no... <jon...@ab...> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail: co...@cn... > Biocomputing unit http://i2pc.es/coss > National Center of Biotechnology (CSIC) > c/Darwin, 3 > Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 > 28049 MADRID (SPAIN) Fax: 34-91-585 4506 > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
From: Carlos O. S. <co...@cn...> - 2018-04-14 08:18:20
|
Dear Jonathan, phase shift was not calculated in v1.1, it has been added in the development branch, and it will be present in next release. Kind regards, Carlos Oscar On 13/04/2018 0:59, Jonathan Remis wrote: > > Hello, > > I am using SCIPION v1.1 and want to use a streaming data pipeline to > give me a live readout of phase shifts as I collect images using > gctf. Unlike most of the other information determined in the CTF > estimation I don't see any columns for phase shift. I do see the > values in > > //Runs/xxx_ProtGctf/extra/micrograph_name/ctfEstimation.txt / > / > / > Perhaps there is a way to extract this data from the file but the > format of the file doesn't allow me to grep it, or at least I don't > know how to do this. > > If I am overlooking something or if you know of a way I could more > easily get this information it would be quite useful. > > > Thanks for your help< > Jonathan > > > -- > > ------------------------------------------------------------------------ > > *JONATHAN REMIS* > > CryoEM Facilities Manager > > > Northwestern University > > Department of Molecular Biosciences > > > mailing address > > 2205 Tech Drive > > Hogan 2-100 > > Evanston, IL 60208-3500 > > USA > > > *OFFICE*+1-847-491-7813 > > *EMAIL *jon...@no... <mailto:jon...@ab...> > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://i2pc.es/coss National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
From: Pablo C. <pc...@cn...> - 2018-04-13 05:58:32
|
Hi Jonathan, I believe in v1.1 some of the ctf estimation methods were handling the phaseshift properly and also registering that value in Scipion (might be part of the hidden columns). But until 1.2 (recently released) I don't think we were propagating the phaseshift properly to the rest of the later processing. Please, someone correct me if I'm wrong. What I know is that we have reviewed the phaseshift management for v1.2 and done some processing succesfully, that before, with 1.1, it didn't render nice results. So, my suggestion would be to update your scipion version to 1.2. We made the effort to keep backwards compatibility, so I don't expect you to start your project from scratch. All the best, Pablo. Scipion team. On 13/04/18 00:59, Jonathan Remis wrote: > > Hello, > > I am using SCIPION v1.1 and want to use a streaming data pipeline to > give me a live readout of phase shifts as I collect images using > gctf. Unlike most of the other information determined in the CTF > estimation I don't see any columns for phase shift. I do see the > values in > > //Runs/xxx_ProtGctf/extra/micrograph_name/ctfEstimation.txt / > / > / > Perhaps there is a way to extract this data from the file but the > format of the file doesn't allow me to grep it, or at least I don't > know how to do this. > > If I am overlooking something or if you know of a way I could more > easily get this information it would be quite useful. > > > Thanks for your help< > Jonathan > > > -- > > ------------------------------------------------------------------------ > > *JONATHAN REMIS* > > CryoEM Facilities Manager > > > Northwestern University > > Department of Molecular Biosciences > > > mailing address > > 2205 Tech Drive > > Hogan 2-100 > > Evanston, IL 60208-3500 > > USA > > > *OFFICE*+1-847-491-7813 > > *EMAIL *jon...@no... <mailto:jon...@ab...> > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
From: Jonathan R. <jon...@no...> - 2018-04-12 23:00:15
|
Hello, I am using SCIPION v1.1 and want to use a streaming data pipeline to give me a live readout of phase shifts as I collect images using gctf. Unlike most of the other information determined in the CTF estimation I don't see any columns for phase shift. I do see the values in */Runs/xxx_ProtGctf/extra/micrograph_name/ctfEstimation.txt * Perhaps there is a way to extract this data from the file but the format of the file doesn't allow me to grep it, or at least I don't know how to do this. If I am overlooking something or if you know of a way I could more easily get this information it would be quite useful. Thanks for your help< Jonathan -- ------------------------------ *JONATHAN REMIS* CryoEM Facilities Manager Northwestern University Department of Molecular Biosciences mailing address 2205 Tech Drive Hogan 2-100 Evanston, IL 60208-3500 USA *OFFICE* +1-847-491-7813 *EMAIL * jon...@no... <jon...@ab...> |
From: Per A B. <p.b...@sh...> - 2018-04-12 14:27:36
|
How much do you think travel and accommodation will cost? Per On 4 April 2018 at 15:19:32, Pablo Conesa (pc...@cn...) wrote: Dear EM Community, The Instruct Image Processing Center (I2PC) at MadridI2PC is organizing its second *Cryo-EM Facilities meeting*, following the successful first meeting hold last year. The aim is to gather together Cryo-EM *Facility managers* who want to share their experience, problems and solutions on data handling and processing, using Scipion or not. I2PC, as developers of Scipion, has as one of its top priorities the improvement of the functionality that Scipion offers to Cryo-EM Facilities. We will present Scipion and how it is used in several Facilities, such as Diamond/eBIC (UK), ESRF (FR and International), SciLifeLab (Sweden), NIH at NCI (US), NIH at NIEHS (US) or McGill University (Canada) (click here for a map of Facilities using Scipion <https://www.google.com/maps/d/viewer?mid=1MHEnnhBsUarOGJnlo0BapQrrGtA&hl=es&usp=sharing>); We will also count with FEI/Thermo-Fisher participation in the context of the I2PC-FEI Image Processing Course on Scipion for Facilities that will immediately follow this meeting. We will present Scipion 2018-2019 Road Map during the meeting, so that Facilities could comment and improve on it. together with its development Road Map. More importantly, there will be ample time to discuss and present common Facility data handling and processing problems, and hopefully share with others how you are running your Facility in those aspects. For more details, please go here <http://i2pc.es/2nd-i2pc-cryoem-facilities-meeting-madrid-june-26-27-2018/>. All the best, Pablo. Scipion team - I2PC center _______________________________________________ 3dem mailing list 3d...@nc... https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem |
From: abhisek M. <abh...@gm...> - 2018-04-07 06:27:03
|
Hi, My Relion-2.1 in scipion keep raising this error: *[localhost.localdomain:05066] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005* *00036: *** An error occurred in MPI_Init* *00037: *** on a NULL communicator* *00038: *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,* *00039: *** and potentially your MPI job)* *00040: [localhost.localdomain:5066] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!* What is surprising to me is Xmipp3-cl2d is running alright in MPI but Relion-2D classification is getting crashed. Please help me out here. thank you -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* |
From: Carlos O. S. <co...@cn...> - 2018-04-06 22:00:48
|
This is a common question. In CL2D, and in principle all other 2D classifiers, you may see the average, standard deviation and FSC of any class. For doing so, 1) open the images behind the class you are interested in 2) make sure that the geometry is applied (Display -> Apply Geometry) 3) Calculate the avg or FSC (Tools -> ...) The FSC is shown in digital frequency. The sampling rate in this example was 2.12A/pix and the FSC drops below 0.5 at about w=0.075. Then, the continuous resolution associated to this class is 2.12/0.075=28A. See attachment. Kind regards, Carlos Oscar -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://i2pc.es/coss National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |