scipion-users — Mailing list for Scipion users

[scipion-users] fix for___%Y-%m-%d %H:%M:%S.%

[D.A. S. <sem...@gm...>]

Dear colleagues,

Is there an easy fix for such an error that occur when you switch 
between the SCIPION versions?

time data '2017-11-03 23:17:36' does not match format '%Y-%m-%d 
%H:%M:%S.%f'

Thank you!

Sincerely,
Dmitry

Re: [scipion-users] Xmipp workflow test failure

[John H. <joh...@co...>]

Thanks, Jose Miguel!

Regards,
-jh-

On 10/28/2017 09:01 AM, Jose Miguel de la Rosa Trevin wrote:
> Hi John,
>
> Thanks for your feedback. As you already guessed, the binaries are 
> compiled against
> a given version of libmpi (if I remember correctly we are using a 
> CentOS  6 or similar).
> So, I think that if you build from source it should properly link to 
> the correct libmpi version.
>
> Let us know if that work for you or any other idea.
>
> Cheers,
> Jose Miguel
>
>
> On Sat, Oct 28, 2017 at 8:12 AM, John Heumann 
> <joh...@co... <mailto:joh...@co...>> wrote:
>
>     Greetings!
>
>     I recently installed the v1.1_2017-06-14  binaries on a RHEL7
>     system.  None of the additional packages are currently installed.
>     All of the small tests pass except 2 which seem to be using eman
>     components (not installed), so I'm ignoring those. The Xmipp
>     workflow test failed at the ML2D step, however. The stdout log
>     indicates failure to load libmpi.so.1. It's not surprising that it
>     can't find libmpi.so.1 since the current version is
>     libmpi.so.12.0.6. As a temporary workaround I made a symbolic link
>     libmpi.so.1 -> libmpi.so, which, in turn, points to
>     libmpi.so.12.06. The test passes after this kludge.
>
>     Why is this test trying to load a specific, older version of the
>     mpi library? Isn't  the core functionality in the newer versions
>     backwards compatible?  Would I avoid this problem if I build from
>     source myself? Or have I configured something incorrectly?
>
>     Thanks in advance!
>
>     Regards,
>     -jh-
>
>     -- 
>     John M. Heumann
>     Department of Molecular, Cellular, and Developmental Biology
>     347 UCB, University of Colorado
>     Boulder, CO 80309-0347
>
>
>     ------------------------------------------------------------------------------
>     Check out the vibrant tech community on one of the world's most
>     engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>     <http://secure-web.cisco.com/1SgICm5s5ROsvLzhZDbbmQbgUlWoAsmQGisPXKJhqM7gLWMRBu9lkMNB_4v7WnvpF2J4vgYdnci1a_JicQl8K3fzuNTq8Ufy0P6Nc9rzgYsuRXhNwF9zNEZ8vZ5118fgG2TVHAB-DsEOBTp8i7DkZ7BdcF1vCZzB0KTc9Tk9QFfq5os_HuzBYw_jKol2H0pHHHYa2sMVfx-pkaAW0y4a_M7yFzLGNb_2UWoqu1LKzWZuBh968WLp8_BzEobivUY_4vRBQ1sNjzQGdoa1EM0pCPMOoFU-JR_nP6yEI0C9RCp2Y6vVFc3GFb4baePHErS2lziViYzk68bG4_EI8bBrbO6xNv6VSlwVXlKB321QODVP4qHu15F2Zcx_AiMPaLy13_e-ve-TCWbt5-ZmGtkU4tTJfW2wrfZRMKwXyEPMttEL5PY6_1s3vlI3X3g3Kn_bgHltLdQNislKJSG4NKNF4UQ/http%3A%2F%2Fsdm.link%2Fslashdot>
>     _______________________________________________
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>     sci...@li...
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>
>

-- 
John M. Heumann
Department of Molecular, Cellular, and Developmental Biology
347 UCB, University of Colorado
Boulder, CO 80309-0347

Re: [scipion-users] Xmipp workflow test failure

[Jose M. de la R. T. <del...@gm...>]

Hi John,

Thanks for your feedback. As you already guessed, the binaries are compiled
against
a given version of libmpi (if I remember correctly we are using a CentOS  6
or similar).
So, I think that if you build from source it should properly link to the
correct libmpi version.

Let us know if that work for you or any other idea.

Cheers,
Jose Miguel


On Sat, Oct 28, 2017 at 8:12 AM, John Heumann <joh...@co...>
wrote:

> Greetings!
>
> I recently installed the v1.1_2017-06-14  binaries on a RHEL7 system.
> None of the additional packages are currently installed. All of the small
> tests pass except 2 which seem to be using eman components (not installed),
> so I'm ignoring those. The Xmipp workflow test failed at the ML2D step,
> however. The stdout log indicates failure to load libmpi.so.1. It's not
> surprising that it can't find libmpi.so.1 since the current version is
> libmpi.so.12.0.6. As a temporary workaround I made a symbolic link
> libmpi.so.1 -> libmpi.so, which, in turn, points to libmpi.so.12.06. The
> test passes after this kludge.
>
> Why is this test trying to load a specific, older version of the mpi
> library? Isn't  the core functionality in the newer versions backwards
> compatible?  Would I avoid this problem if I build from source myself? Or
> have I configured something incorrectly?
>
> Thanks in advance!
>
> Regards,
> -jh-
>
> --
> John M. Heumann
> Department of Molecular, Cellular, and Developmental Biology
> 347 UCB, University of Colorado
> Boulder, CO 80309-0347
>
>
> ------------------------------------------------------------
> ------------------
> 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
>

[scipion-users] Xmipp workflow test failure

[John H. <joh...@co...>]

Greetings!

I recently installed the v1.1_2017-06-14  binaries on a RHEL7 system.  
None of the additional packages are currently installed. All of the 
small tests pass except 2 which seem to be using eman components (not 
installed), so I'm ignoring those. The Xmipp workflow test failed at the 
ML2D step, however. The stdout log indicates failure to load 
libmpi.so.1. It's not surprising that it can't find libmpi.so.1 since 
the current version is libmpi.so.12.0.6. As a temporary workaround I 
made a symbolic link libmpi.so.1 -> libmpi.so, which, in turn, points to 
libmpi.so.12.06. The test passes after this kludge.

Why is this test trying to load a specific, older version of the mpi 
library? Isn't  the core functionality in the newer versions backwards 
compatible?  Would I avoid this problem if I build from source myself? 
Or have I configured something incorrectly?

Thanks in advance!

Regards,
-jh-

-- 
John M. Heumann
Department of Molecular, Cellular, and Developmental Biology
347 UCB, University of Colorado
Boulder, CO 80309-0347

Re: [scipion-users] particle polishing

[Grigory S. <sha...@gm...>]

Hi Dmitry,

please check that you have loaded required CUDA module (7.5) and set up
correctly CUDA_BIN and CUDA_LIB in your $SCIPION/config/scipion.conf file.


Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...

On Thu, Oct 19, 2017 at 4:36 PM, D.A. Semchonok <sem...@gm...> wrote:

> Dear Grigory,
>
> So issue with polishing again -
>
> please see the print-screen.
>
> (I was using threads = 20)
>
>
> Any solution/advice?
>
>
>
>
> Thank you!
>
> Sincerely,
> Dmitry
>

Re: [scipion-users] problem with cuda-Relion

[abhisek M. <abh...@gm...>]

Hello,

Is there any way to restrict how much memory will be used from GPU ? I mean
set a cut-off value for GPU.

On Mon, Oct 16, 2017 at 3:38 PM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Hi Abhisek,
>
> You can try to reduce the number of MPI or threads to avoid usage of GPU
> memory.
>
> Hope that helps,
> Best,
> Jose Miguel
>
>
> On Mon, Oct 16, 2017 at 5:36 PM, abhisek Mondal <abh...@gm...>
> wrote:
>
>> Hi,
>>
>> I was running a 3D classification in Relion-2.0 with GPU-acceleration on.
>> But after running sometime it ran out of memory.
>> The error message was following:
>> *00181:    Expectation iteration 3 of 25*
>> *00182:   0.50/36.78 min ~~(,_,">[localhost:05098] *** Process received
>> signal ****
>> *00183:   [localhost:05098] Signal: Segmentation fault (11)*
>> *00184:   [localhost:05098] Signal code: Address not mapped (1)*
>> *00185:   [localhost:05098] Failing at address: 0x28*
>> *00186:   [localhost:05098] [ 0] /lib64/libpthread.so.0(+0xf5e0)
>> [0x7f2a4a5575e0]*
>> *00187:   [localhost:05098] [ 1]
>> /home/user/scipion/software/em/relion-2.0.4/lib/librelion_gpu_util.so(_ZNSt6vectorI10cudaStagerImESaIS1_EED1Ev+0x3d)
>> [0x7f2a4af5195d]*
>> *00188:   [localhost:05098] [ 2]
>> /home/user/scipion/software/em/relion-2.0.4/lib/librelion_gpu_util.so(_ZN15MlOptimiserCuda32doThreadExpectationSomeParticlesEi+0x31a5)
>> [0x7f2a4af4ca15]*
>> *00189:   [localhost:05098] [ 3]
>> /home/user/scipion/software/em/relion-2.0.4/lib/librelion_lib.so(_Z36globalThreadExpectationSomeParticlesR14ThreadArgument+0x28)
>> [0x7f2a556a5a88]*
>> *00190:   [localhost:05098] [ 4]
>> /home/user/scipion/software/em/relion-2.0.4/lib/librelion_lib.so(_Z11_threadMainPv+0x1d)
>> [0x7f2a556d8a6d]*
>> *00191:   [localhost:05098] [ 5] /lib64/libpthread.so.0(+0x7e25)
>> [0x7f2a4a54fe25]*
>> *00192:   [localhost:05098] [ 6] /lib64/libc.so.6(clone+0x6d)
>> [0x7f2a4a27d34d]*
>> *00193:   [localhost:05098] *** End of error message ****
>> *00194:   ERROR: CudaCustomAllocator out of memory*
>> *00195:    [requestedSpace:             82618368 B]*
>> *00196:    [largestContinuousFreeSpace: 35837696 B]*
>> *00197:    [totalFreeSpace:             54575360 B]*
>> *00198:   [512B] (36864B) (165376B) (36864B) (512B) [5632B] (512B) (512B)
>> [1536B] (2048B) [8192B] (36864B) (165376B) [2560B] (2048B) (2048B) [49152B]
>> (165376B) (36864B) (165376B) [55296B] (36864B) (165376B) [540672B] (90112B)
>> (91648B) (90112B) (91648B) (90112B) (91648B) (941056B) [994304B] (2642432B)
>> [3305984B] (19759616B) (39519232B) (39519232B) (39519232B) (39519232B)
>> (79037952B) [13773824B] (24662528B) (49325056B) (49325056B) (49325056B)
>> (49325056B) (98649600B) (20654592B) (41309184B) (41309184B) (41309184B)
>> (41309184B) [35837696B] = 823101184B*
>> *00199:   1.07/40.23 min
>> .~~(,_,">--------------------------------------------------------------------------*
>> *00200:   mpirun noticed that process rank 3 with PID 5098 on node
>> localhost.localdomain exited on signal 11 (Segmentation fault).*
>> *00201:
>> --------------------------------------------------------------------------*
>> *00202:   Traceback (most recent call last):*
>> *00203:     File "/home/user/scipion/pyworkflow/protocol/protocol.py",
>> line 182, in run*
>> *00204:       self._run()*
>> *00205:     File "/home/user/scipion/pyworkflow/protocol/protocol.py",
>> line 228, in _run*
>> *00206:       resultFiles = self._runFunc()*
>> *00207:     File "/home/user/scipion/pyworkflow/protocol/protocol.py",
>> line 224, in _runFunc*
>> *00208:       return self._func(*self._args)*
>> *00209:     File
>> "/home/user/scipion/pyworkflow/em/packages/relion/protocol_base.py", line
>> 789, in runRelionStep*
>> *00210:       self.runJob(self._getProgram(), params)*
>> *00211:     File "/home/user/scipion/pyworkflow/protocol/protocol.py",
>> line 1077, in runJob*
>> *00212:       self._stepsExecutor.runJob(self._log, program, arguments,
>> **kwargs)*
>> *00213:     File "/home/user/scipion/pyworkflow/protocol/executor.py",
>> line 56, in runJob*
>> *00214:       env=env, cwd=cwd)*
>> *00215:     File "/home/user/scipion/pyworkflow/utils/process.py", line
>> 51, in runJob*
>> *00216:       return runCommand(command, env, cwd)*
>> *00217:     File "/home/user/scipion/pyworkflow/utils/process.py", line
>> 65, in runCommand*
>> *00218:       check_call(command, shell=True, stdout=sys.stdout,
>> stderr=sys.stderr, env=env, cwd=cwd)*
>> *00219:     File
>> "/home/user/scipion/software/lib/python2.7/subprocess.py", line 540, in
>> check_call*
>> *00220:       raise CalledProcessError(retcode, cmd)*
>> *00221:   CalledProcessError: Command 'mpirun -np 6 -bynode  `which
>> relion_refine_mpi` --gpu  --pool 3 --angpix 1.89
>> --dont_combine_weights_via_disc  --ctf_phase_flipped  --ref
>> Runs/005404_ProtRelionClassify3D/tmp/threed_06.mrc --scale  --offset_range
>> 5.0 --ini_high 60.0 --offset_step 2.0 --healpix_order 2 --tau2_fudge 4
>> --ctf  --oversampling 1 --o Runs/005404_ProtRelionClassify3D/extra/relion
>> --i Runs/005404_ProtRelionClassify3D/input_particles.star --iter 25
>> --zero_mask  --norm  --firstiter_cc  --sym c1 --K 5 --flatten_solvent
>>  --particle_diameter 242  --j 3' returned non-zero exit status 139*
>>
>> Is there any way to avoid this crash ? Can I restrict GPU memory ?
>>
>> Thank you.
>>
>> --
>> Abhisek Mondal
>>
>> *Senior Research Fellow*
>>
>> *Structural Biology and Bioinformatics Division*
>> *CSIR-Indian Institute of Chemical Biology*
>>
>> *Kolkata 700032*
>>
>> *INDIA*
>>
>> ------------------------------------------------------------
>> ------------------
>> 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
>>
>>
>


-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Re: [scipion-users] problem with cuda-Relion

[Jose M. de la R. T. <del...@gm...>]

Hi Abhisek,

You can try to reduce the number of MPI or threads to avoid usage of GPU
memory.

Hope that helps,
Best,
Jose Miguel


On Mon, Oct 16, 2017 at 5:36 PM, abhisek Mondal <abh...@gm...>
wrote:

> Hi,
>
> I was running a 3D classification in Relion-2.0 with GPU-acceleration on.
> But after running sometime it ran out of memory.
> The error message was following:
> *00181:    Expectation iteration 3 of 25*
> *00182:   0.50/36.78 min ~~(,_,">[localhost:05098] *** Process received
> signal ****
> *00183:   [localhost:05098] Signal: Segmentation fault (11)*
> *00184:   [localhost:05098] Signal code: Address not mapped (1)*
> *00185:   [localhost:05098] Failing at address: 0x28*
> *00186:   [localhost:05098] [ 0] /lib64/libpthread.so.0(+0xf5e0)
> [0x7f2a4a5575e0]*
> *00187:   [localhost:05098] [ 1]
> /home/user/scipion/software/em/relion-2.0.4/lib/librelion_gpu_util.so(_ZNSt6vectorI10cudaStagerImESaIS1_EED1Ev+0x3d)
> [0x7f2a4af5195d]*
> *00188:   [localhost:05098] [ 2]
> /home/user/scipion/software/em/relion-2.0.4/lib/librelion_gpu_util.so(_ZN15MlOptimiserCuda32doThreadExpectationSomeParticlesEi+0x31a5)
> [0x7f2a4af4ca15]*
> *00189:   [localhost:05098] [ 3]
> /home/user/scipion/software/em/relion-2.0.4/lib/librelion_lib.so(_Z36globalThreadExpectationSomeParticlesR14ThreadArgument+0x28)
> [0x7f2a556a5a88]*
> *00190:   [localhost:05098] [ 4]
> /home/user/scipion/software/em/relion-2.0.4/lib/librelion_lib.so(_Z11_threadMainPv+0x1d)
> [0x7f2a556d8a6d]*
> *00191:   [localhost:05098] [ 5] /lib64/libpthread.so.0(+0x7e25)
> [0x7f2a4a54fe25]*
> *00192:   [localhost:05098] [ 6] /lib64/libc.so.6(clone+0x6d)
> [0x7f2a4a27d34d]*
> *00193:   [localhost:05098] *** End of error message ****
> *00194:   ERROR: CudaCustomAllocator out of memory*
> *00195:    [requestedSpace:             82618368 B]*
> *00196:    [largestContinuousFreeSpace: 35837696 B]*
> *00197:    [totalFreeSpace:             54575360 B]*
> *00198:   [512B] (36864B) (165376B) (36864B) (512B) [5632B] (512B) (512B)
> [1536B] (2048B) [8192B] (36864B) (165376B) [2560B] (2048B) (2048B) [49152B]
> (165376B) (36864B) (165376B) [55296B] (36864B) (165376B) [540672B] (90112B)
> (91648B) (90112B) (91648B) (90112B) (91648B) (941056B) [994304B] (2642432B)
> [3305984B] (19759616B) (39519232B) (39519232B) (39519232B) (39519232B)
> (79037952B) [13773824B] (24662528B) (49325056B) (49325056B) (49325056B)
> (49325056B) (98649600B) (20654592B) (41309184B) (41309184B) (41309184B)
> (41309184B) [35837696B] = 823101184B*
> *00199:   1.07/40.23 min
> .~~(,_,">--------------------------------------------------------------------------*
> *00200:   mpirun noticed that process rank 3 with PID 5098 on node
> localhost.localdomain exited on signal 11 (Segmentation fault).*
> *00201:
> --------------------------------------------------------------------------*
> *00202:   Traceback (most recent call last):*
> *00203:     File "/home/user/scipion/pyworkflow/protocol/protocol.py",
> line 182, in run*
> *00204:       self._run()*
> *00205:     File "/home/user/scipion/pyworkflow/protocol/protocol.py",
> line 228, in _run*
> *00206:       resultFiles = self._runFunc()*
> *00207:     File "/home/user/scipion/pyworkflow/protocol/protocol.py",
> line 224, in _runFunc*
> *00208:       return self._func(*self._args)*
> *00209:     File
> "/home/user/scipion/pyworkflow/em/packages/relion/protocol_base.py", line
> 789, in runRelionStep*
> *00210:       self.runJob(self._getProgram(), params)*
> *00211:     File "/home/user/scipion/pyworkflow/protocol/protocol.py",
> line 1077, in runJob*
> *00212:       self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)*
> *00213:     File "/home/user/scipion/pyworkflow/protocol/executor.py",
> line 56, in runJob*
> *00214:       env=env, cwd=cwd)*
> *00215:     File "/home/user/scipion/pyworkflow/utils/process.py", line
> 51, in runJob*
> *00216:       return runCommand(command, env, cwd)*
> *00217:     File "/home/user/scipion/pyworkflow/utils/process.py", line
> 65, in runCommand*
> *00218:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr, env=env, cwd=cwd)*
> *00219:     File
> "/home/user/scipion/software/lib/python2.7/subprocess.py", line 540, in
> check_call*
> *00220:       raise CalledProcessError(retcode, cmd)*
> *00221:   CalledProcessError: Command 'mpirun -np 6 -bynode  `which
> relion_refine_mpi` --gpu  --pool 3 --angpix 1.89
> --dont_combine_weights_via_disc  --ctf_phase_flipped  --ref
> Runs/005404_ProtRelionClassify3D/tmp/threed_06.mrc --scale  --offset_range
> 5.0 --ini_high 60.0 --offset_step 2.0 --healpix_order 2 --tau2_fudge 4
> --ctf  --oversampling 1 --o Runs/005404_ProtRelionClassify3D/extra/relion
> --i Runs/005404_ProtRelionClassify3D/input_particles.star --iter 25
> --zero_mask  --norm  --firstiter_cc  --sym c1 --K 5 --flatten_solvent
>  --particle_diameter 242  --j 3' returned non-zero exit status 139*
>
> Is there any way to avoid this crash ? Can I restrict GPU memory ?
>
> Thank you.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>
> ------------------------------------------------------------
> ------------------
> 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
>
>

[scipion-users] problem with cuda-Relion

[abhisek M. <abh...@gm...>]

Hi,

I was running a 3D classification in Relion-2.0 with GPU-acceleration on.
But after running sometime it ran out of memory.
The error message was following:
*00181:    Expectation iteration 3 of 25*
*00182:   0.50/36.78 min ~~(,_,">[localhost:05098] *** Process received
signal ****
*00183:   [localhost:05098] Signal: Segmentation fault (11)*
*00184:   [localhost:05098] Signal code: Address not mapped (1)*
*00185:   [localhost:05098] Failing at address: 0x28*
*00186:   [localhost:05098] [ 0] /lib64/libpthread.so.0(+0xf5e0)
[0x7f2a4a5575e0]*
*00187:   [localhost:05098] [ 1]
/home/user/scipion/software/em/relion-2.0.4/lib/librelion_gpu_util.so(_ZNSt6vectorI10cudaStagerImESaIS1_EED1Ev+0x3d)
[0x7f2a4af5195d]*
*00188:   [localhost:05098] [ 2]
/home/user/scipion/software/em/relion-2.0.4/lib/librelion_gpu_util.so(_ZN15MlOptimiserCuda32doThreadExpectationSomeParticlesEi+0x31a5)
[0x7f2a4af4ca15]*
*00189:   [localhost:05098] [ 3]
/home/user/scipion/software/em/relion-2.0.4/lib/librelion_lib.so(_Z36globalThreadExpectationSomeParticlesR14ThreadArgument+0x28)
[0x7f2a556a5a88]*
*00190:   [localhost:05098] [ 4]
/home/user/scipion/software/em/relion-2.0.4/lib/librelion_lib.so(_Z11_threadMainPv+0x1d)
[0x7f2a556d8a6d]*
*00191:   [localhost:05098] [ 5] /lib64/libpthread.so.0(+0x7e25)
[0x7f2a4a54fe25]*
*00192:   [localhost:05098] [ 6] /lib64/libc.so.6(clone+0x6d)
[0x7f2a4a27d34d]*
*00193:   [localhost:05098] *** End of error message ****
*00194:   ERROR: CudaCustomAllocator out of memory*
*00195:    [requestedSpace:             82618368 B]*
*00196:    [largestContinuousFreeSpace: 35837696 B]*
*00197:    [totalFreeSpace:             54575360 B]*
*00198:   [512B] (36864B) (165376B) (36864B) (512B) [5632B] (512B) (512B)
[1536B] (2048B) [8192B] (36864B) (165376B) [2560B] (2048B) (2048B) [49152B]
(165376B) (36864B) (165376B) [55296B] (36864B) (165376B) [540672B] (90112B)
(91648B) (90112B) (91648B) (90112B) (91648B) (941056B) [994304B] (2642432B)
[3305984B] (19759616B) (39519232B) (39519232B) (39519232B) (39519232B)
(79037952B) [13773824B] (24662528B) (49325056B) (49325056B) (49325056B)
(49325056B) (98649600B) (20654592B) (41309184B) (41309184B) (41309184B)
(41309184B) [35837696B] = 823101184B*
*00199:   1.07/40.23 min
.~~(,_,">--------------------------------------------------------------------------*
*00200:   mpirun noticed that process rank 3 with PID 5098 on node
localhost.localdomain exited on signal 11 (Segmentation fault).*
*00201:
--------------------------------------------------------------------------*
*00202:   Traceback (most recent call last):*
*00203:     File "/home/user/scipion/pyworkflow/protocol/protocol.py", line
182, in run*
*00204:       self._run()*
*00205:     File "/home/user/scipion/pyworkflow/protocol/protocol.py", line
228, in _run*
*00206:       resultFiles = self._runFunc()*
*00207:     File "/home/user/scipion/pyworkflow/protocol/protocol.py", line
224, in _runFunc*
*00208:       return self._func(*self._args)*
*00209:     File
"/home/user/scipion/pyworkflow/em/packages/relion/protocol_base.py", line
789, in runRelionStep*
*00210:       self.runJob(self._getProgram(), params)*
*00211:     File "/home/user/scipion/pyworkflow/protocol/protocol.py", line
1077, in runJob*
*00212:       self._stepsExecutor.runJob(self._log, program, arguments,
**kwargs)*
*00213:     File "/home/user/scipion/pyworkflow/protocol/executor.py", line
56, in runJob*
*00214:       env=env, cwd=cwd)*
*00215:     File "/home/user/scipion/pyworkflow/utils/process.py", line 51,
in runJob*
*00216:       return runCommand(command, env, cwd)*
*00217:     File "/home/user/scipion/pyworkflow/utils/process.py", line 65,
in runCommand*
*00218:       check_call(command, shell=True, stdout=sys.stdout,
stderr=sys.stderr, env=env, cwd=cwd)*
*00219:     File "/home/user/scipion/software/lib/python2.7/subprocess.py",
line 540, in check_call*
*00220:       raise CalledProcessError(retcode, cmd)*
*00221:   CalledProcessError: Command 'mpirun -np 6 -bynode  `which
relion_refine_mpi` --gpu  --pool 3 --angpix 1.89
--dont_combine_weights_via_disc  --ctf_phase_flipped  --ref
Runs/005404_ProtRelionClassify3D/tmp/threed_06.mrc --scale  --offset_range
5.0 --ini_high 60.0 --offset_step 2.0 --healpix_order 2 --tau2_fudge 4
--ctf  --oversampling 1 --o Runs/005404_ProtRelionClassify3D/extra/relion
--i Runs/005404_ProtRelionClassify3D/input_particles.star --iter 25
--zero_mask  --norm  --firstiter_cc  --sym c1 --K 5 --flatten_solvent
 --particle_diameter 242  --j 3' returned non-zero exit status 139*

Is there any way to avoid this crash ? Can I restrict GPU memory ?

Thank you.

-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Re: [scipion-users] starting up the SCIPION dev

[Grigory S. <sha...@gm...>]

Dear Dmitry,

I guess this is related with the upgrade to CentOS 7. Your issue is
described here: https://www.centos.org/forums/viewtopic.php?t=48723

You should ask your sysadmin to create a symlink for missing library
(libptf77blas.so.3) pointing to libtatlas.so. Hopefully, this will solve
the problem.


Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...

On Wed, Oct 11, 2017 at 3:48 PM, D.A. Semchonok <sem...@gm...> wrote:

> Dear Grigory,
>
> I would like to ask if you possibly know what may go wrong in starting up
> of the SCIPON dev and how can I fix that.
>
> When I start up the software I get the following error:
>
>
> Thank you!
>
> Sincerely,
> Dmitry
>
>
>
>
>

Re: [scipion-users] Scipion Install: CMake fails for lapack, gcc/gfortran linking problem?

[Grigory S. <sha...@gm...>]

Hello Teige,

just a wild guess: from what I can see you are using eman2 cmake instead of
the system one. Have you tried removing any eman-related stuff from your
environment and trying to recompile?

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...

On Fri, Sep 29, 2017 at 5:49 PM, Matthews-Palmer, Teige Rowan Seal <
t.m...@im...> wrote:

> Dear Scipion users,
>
>
> I wondered if anyone can suggest a solution to a problem I'm having
> compiling Scipion from a clone of the git on Linux Mint 17.3.
>
>
> gcc & gfortran are both version 4.8.4
>
> cmake is version 2.8.12.2
>
>
> scipion install proceeds until:
>
>
> cd software/tmp/lapack-3.5.0
> cmake -DBUILD_SHARED_LIBS:BOOL=ON -DLAPACKE:BOOL=ON
> -DCMAKE_INSTALL_PREFIX:PATH=/beebylab/software/scipion/1.1/software . >
> /beebylab/software/scipion/1.1/software/log/lapack_cmake.log 2>&1
> Error: target 'software/tmp/lapack-3.5.0/Makefile' not built
>
>
> Looking at the CMake log, it says gcc is broken and unable to compile a
> test:
>
> cat /beebylab/software/scipion/1.1/software/log/lapack_cmake.log
> -- The Fortran compiler identification is GNU 4.8.4
> -- Check for working Fortran compiler: /usr/bin/gcc
> -- Check for working Fortran compiler: /usr/bin/gcc  -- broken
> CMake Error at /beebylab/software/eman/EMAN2.2/share/cmake-3.8/Modules/
> CMakeTestFortranCompiler.cmake:44 (message):
>   The Fortran compiler "/usr/bin/gcc" is not able to compile a simple test
>   program.
>
>
> Looking at the CMake Error log to see the cause, apparently all the calls
> of gfortran procedures in the test fortran script are 'undefined' (problem
> with linking or paths but I don't understand this well, no experience of
> make or cmake).
>
> e.g. (selection of lines not in proper order, that illustrate things not
> found)
>
> gcc: error trying to exec 'f951': execvp: No such file or directory
>
> CMakeFortranCompilerId.F:(.text+0x93f): undefined reference to
> `_gfortran_st_write'
> CMakeFortranCompilerId.F:(.text+0x958): undefined reference to
> `_gfortran_transfer_character_write'
> CMakeFortranCompilerId.F:(.text+0x967): undefined reference to
> `_gfortran_st_write_done'
> testFortranCompiler.f:(.text+0x3f): undefined reference to
> `_gfortran_st_write'
> testFortranCompiler.f:(.text+0x58): undefined reference to
> `_gfortran_transfer_character_write'
> testFortranCompiler.f:(.text+0x67): undefined reference to
> `_gfortran_st_write_done'
>
>
> I'll attach the entire error log, but it's very long. Any suggestions are
> really appreciated!
>
> All the best
>
> Teige
>
>
>
>
>
>
> ------------------------------------------------------------
> ------------------
> 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
>
>

[scipion-users] Scipion Install: CMake fails for lapack, gcc/gfortran linking problem?

[Matthews-Palmer, T. R. S. <t.m...@im...>]

Dear Scipion users,


I wondered if anyone can suggest a solution to a problem I'm having compiling Scipion from a clone of the git on Linux Mint 17.3.


gcc & gfortran are both version 4.8.4

cmake is version 2.8.12.2


scipion install proceeds until:

cd software/tmp/lapack-3.5.0
cmake -DBUILD_SHARED_LIBS:BOOL=ON -DLAPACKE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/beebylab/software/scipion/1.1/software . > /beebylab/software/scipion/1.1/software/log/lapack_cmake.log 2>&1
Error: target 'software/tmp/lapack-3.5.0/Makefile' not built


Looking at the CMake log, it says gcc is broken and unable to compile a test:

cat /beebylab/software/scipion/1.1/software/log/lapack_cmake.log
-- The Fortran compiler identification is GNU 4.8.4
-- Check for working Fortran compiler: /usr/bin/gcc
-- Check for working Fortran compiler: /usr/bin/gcc  -- broken
CMake Error at /beebylab/software/eman/EMAN2.2/share/cmake-3.8/Modules/CMakeTestFortranCompiler.cmake:44 (message):
  The Fortran compiler "/usr/bin/gcc" is not able to compile a simple test
  program.


Looking at the CMake Error log to see the cause, apparently all the calls of gfortran procedures in the test fortran script are 'undefined' (problem with linking or paths but I don't understand this well, no experience of make or cmake).

e.g. (selection of lines not in proper order, that illustrate things not found)

gcc: error trying to exec 'f951': execvp: No such file or directory

CMakeFortranCompilerId.F:(.text+0x93f): undefined reference to `_gfortran_st_write'
CMakeFortranCompilerId.F:(.text+0x958): undefined reference to `_gfortran_transfer_character_write'
CMakeFortranCompilerId.F:(.text+0x967): undefined reference to `_gfortran_st_write_done'
testFortranCompiler.f:(.text+0x3f): undefined reference to `_gfortran_st_write'
testFortranCompiler.f:(.text+0x58): undefined reference to `_gfortran_transfer_character_write'
testFortranCompiler.f:(.text+0x67): undefined reference to `_gfortran_st_write_done'


I'll attach the entire error log, but it's very long. Any suggestions are really appreciated!

All the best

Teige

Re: [scipion-users] Scipion for MacOS

[Jose M. de la R. T. <del...@gm...>]

Dear Guixing,

Thanks for your feedback, it is important for us to know better the user
needs.
We will try our best to have a Mac version, but as Pablo said, we still
have many
other things to deal with before.

Best,
Jose Miguel


On Thu, Sep 14, 2017 at 10:20 AM, Pablo Conesa <pc...@cn...> wrote:

> Dear Guixing Ma
>
> We have done some attempts and were unsuccessful. It's in our "TO DO" list
> but I must say is not a priority...unless we see more and more request like
> yours.
>
> All the best, Pablo.
>
> Scipion team
>
> On 14/09/17 09:51, 马贵兴 wrote:
>
> Dear sir/miss:
>
> I strongly suggest you to make an MacOS version of Scipion.
>
> May I known if you have the plan？
>
> Many thanks.
>
> yours.
>
>
> 马贵兴
> Guixing Ma
> 南方科技大学生物系
> Department of Biology, South University of Science and Technology of China
> E-mail:ma...@ma...
> Tel:18575522114 <(857)%20552-2114>
> 地址：广东省深圳市南山区西丽学苑大道1088号
> Addr: 1088 Xueyuan Road, Nanshan District, Shenzhen, Guangdong, China
>
>
> ------------------------------------------------------------------------------
> 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
>
>
>
> ------------------------------------------------------------
> ------------------
> 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
>
>

Re: [scipion-users] Scipion for MacOS

[Pablo C. <pc...@cn...>]

Dear Guixing Ma

We have done some attempts and were unsuccessful. It's in our "TO DO" 
list but I must say is not a priority...unless we see more and more 
request like yours.

All the best, Pablo.

Scipion team


On 14/09/17 09:51, 马贵兴 wrote:
>
> Dear sir/miss:
>
> I strongly suggest you to make an MacOS version of Scipion.
>
> May I known if you have the plan？
>
> Many thanks.
>
> yours.
>
>
> 马贵兴
> Guixing Ma
> 南方科技大学生物系
> Department of Biology, South University of Science and Technology of 
> China
> E-mail:ma...@ma... <mailto:ma...@ma...>
> Tel:18575522114
> 地址：广东省深圳市南山区西丽学苑大道1088号
> Addr: 1088 Xueyuan Road, Nanshan District, Shenzhen, Guangdong, China
>
>
> ------------------------------------------------------------------------------
> 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

[scipion-users] Scipion for MacOS

[<ma...@ma...>]

Dear sir/miss:
I strongly suggest you to make an MacOS version of Scipion.
May I known if you have the plan？
Many thanks.
yours.


马贵兴
Guixing Ma
南方科技大学生物系
Department of Biology, South University of Science and Technology of China
E-mail:ma...@ma...
Tel:18575522114
地址：广东省深圳市南山区西丽学苑大道1088号
Addr: 1088 Xueyuan Road, Nanshan District, Shenzhen, Guangdong, China

Re: [scipion-users] importing from eman2

[Grigory S. <sha...@gm...>]

Hello Abhisek,

I am afraid importing particles from EMAN is not implemented yet. You can
convert *.lst to a new hdf stack and import it using "From files" option,
but no metadata information will be gathered (alignments, CTF).

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...

On Wed, Sep 13, 2017 at 2:41 PM, abhisek Mondal <abh...@gm...>
wrote:

> Hi,
>
> I'm currently trying to import particles from eman2 to scipion. The
> "import particles" option is not allowing simply to import from Eman2.
>
> Can you please help me out here ? I tried but failed to import the *.lst
> file, the all particle stack generated in eman2.
>
> Thank you.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>
> ------------------------------------------------------------
> ------------------
> 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
>
>

[scipion-users] importing from eman2

[abhisek M. <abh...@gm...>]

Hi,

I'm currently trying to import particles from eman2 to scipion. The "import
particles" option is not allowing simply to import from Eman2.

Can you please help me out here ? I tried but failed to import the *.lst
file, the all particle stack generated in eman2.

Thank you.

-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Re: [scipion-users] problem using queuing system

[Juha H. <ju...@st...>]

Hi Gary,

Please contact me directly if you are still struggling with it and I can
share our host.conf file for Univa Grid Engine with you.

Best wishes,
Juha

On Wed, Sep 13, 2017 at 9:23 AM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Hi Gary,
>
> I think I know what the problem is. You need to specify 'localhost' in the
> host.conf file.
> I know it could be a bit confusing and we may improve this in the future.
> It should be able to submit the jobs in your cluster. The _launchRemote
> function in the
> Python code is not fully working. It will be used for a future idea of
> launching jobs
> to more than one machines (clusters or not), but this is still not working.
>
> Best,
> Jose Miguel
>
>
>
> On Tue, Sep 12, 2017 at 10:37 PM, Gary Smith <gar...@vr...> wrote:
>
>> This is what a normal qsub does when you submit a script to UGE...
>>
>> $ qsub busy.sh
>> Your job 6836 ("bz") has been submitted
>> $
>>
>> From: Jose Miguel de la Rosa Trevin <del...@gm...>
>> Date: Tuesday, September 12, 2017 at 4:34 PM
>> To: Vertex <gar...@vr...>
>> Cc: "sci...@li..." <sci...@li...urcefor
>> ge.net>
>> Subject: Re: [scipion-users] problem using queuing system
>>
>> Hi Gary,
>>
>> This error is because Scipion is trying to parse the output from the
>> submission command. It tries to parse a number (the job id) from the
>> output. Can you share the output of a successful submission command to the
>> queue? This could give us a hint about the issue.
>>
>> Best,
>> Jose Miguel
>>
>>
>>
>> On Sep 12, 2017 8:53 PM, "Gary Smith" <gar...@vr...> wrote:
>>
>>> I'm trying to get Scipion-1.1 running with our Univa Grid Engine setup
>>> (aka. SGE).  Scipion appears to be failing to use the launch protocol
>>> remotely, even though this works fine outside of Scipion.  Has anyone seen
>>> errors like this?
>>>
>>> Error during EXECUTE: ** Couldn't parse ouput: [31m
>>> Scipion v1.1 (2017-06-14) Balbino
>>>
>>> [0m
>>>
>>> Traceback:
>>> Traceback (most recent call last):
>>>   File "/cluster/app/scipion/1.1/pyworkflow/gui/form.py", line 1710, in
>>> _close
>>>     message = self.callback(self.protocol, onlySave)
>>>   File "/cluster/app/scipion/1.1/pyworkflow/gui/project/viewprotocols.py",
>>> line 1662, in _executeSaveProtocol
>>>     self.project.launchProtocol(prot)
>>>   File "/cluster/app/scipion/1.1/pyworkflow/project.py", line 417, in
>>> launchProtocol
>>>     pwprot.launch(protocol, wait)
>>>   File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line
>>> 64, in launch
>>>     jobId = _launchRemote(protocol, wait)
>>>   File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line
>>> 164, in _launchRemote
>>>     raise Exception("** Couldn't parse ouput: %s" % redStr(out))
>>> Exception: ** Couldn't parse ouput: [31m
>>> Scipion v1.1 (2017-06-14) Balbino
>>>
>>> [0m
>>>
>>>
>>>
>>> This email message and any attachments are confidential and intended for
>>> use by the addressee(s) only. If you are not the intended recipient, please
>>> notify me immediately by replying to this message, and destroy all copies
>>> of this message and any attachments. Thank you.
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> 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=DwMFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=8Ew8fGcAZAtsnfoFySJ7h_Uw6QpVzYku_PYJB0pVyvc&m=_pTUgPWTKKdSH0G97_STmem_ngcaD_W7ouXimd5uZEU&s=5jVAIqfoH9LR-n1BYFg-4vH_F732aUkGy2qBZORp1Ys&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=DwMFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=8Ew8fGcAZAtsnfoFySJ7h_Uw6QpVzYku_PYJB0pVyvc&m=_pTUgPWTKKdSH0G97_STmem_ngcaD_W7ouXimd5uZEU&s=ewScVJ6V8ISAwcmHqXU8Cuh24C-rS_pS03XGg3-LB1s&e=>
>>>
>>>
>>
>> This email message and any attachments are confidential and intended for
>> use by the addressee(s) only. If you are not the intended recipient, please
>> notify me immediately by replying to this message, and destroy all copies
>> of this message and any attachments. Thank you.
>>
>
>
> ------------------------------------------------------------
> ------------------
> 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
>
>

Re: [scipion-users] problem using queuing system

[Jose M. de la R. T. <del...@gm...>]

Hi Gary,

I think I know what the problem is. You need to specify 'localhost' in the
host.conf file.
I know it could be a bit confusing and we may improve this in the future.
It should be able to submit the jobs in your cluster. The _launchRemote
function in the
Python code is not fully working. It will be used for a future idea of
launching jobs
to more than one machines (clusters or not), but this is still not working.

Best,
Jose Miguel



On Tue, Sep 12, 2017 at 10:37 PM, Gary Smith <gar...@vr...> wrote:

> This is what a normal qsub does when you submit a script to UGE...
>
> $ qsub busy.sh
> Your job 6836 ("bz") has been submitted
> $
>
> From: Jose Miguel de la Rosa Trevin <del...@gm...>
> Date: Tuesday, September 12, 2017 at 4:34 PM
> To: Vertex <gar...@vr...>
> Cc: "sci...@li..." <scipion-users@lists.
> sourceforge.net>
> Subject: Re: [scipion-users] problem using queuing system
>
> Hi Gary,
>
> This error is because Scipion is trying to parse the output from the
> submission command. It tries to parse a number (the job id) from the
> output. Can you share the output of a successful submission command to the
> queue? This could give us a hint about the issue.
>
> Best,
> Jose Miguel
>
>
>
> On Sep 12, 2017 8:53 PM, "Gary Smith" <gar...@vr...> wrote:
>
>> I'm trying to get Scipion-1.1 running with our Univa Grid Engine setup
>> (aka. SGE).  Scipion appears to be failing to use the launch protocol
>> remotely, even though this works fine outside of Scipion.  Has anyone seen
>> errors like this?
>>
>> Error during EXECUTE: ** Couldn't parse ouput: [31m
>> Scipion v1.1 (2017-06-14) Balbino
>>
>> [0m
>>
>> Traceback:
>> Traceback (most recent call last):
>>   File "/cluster/app/scipion/1.1/pyworkflow/gui/form.py", line 1710, in
>> _close
>>     message = self.callback(self.protocol, onlySave)
>>   File "/cluster/app/scipion/1.1/pyworkflow/gui/project/viewprotocols.py",
>> line 1662, in _executeSaveProtocol
>>     self.project.launchProtocol(prot)
>>   File "/cluster/app/scipion/1.1/pyworkflow/project.py", line 417, in
>> launchProtocol
>>     pwprot.launch(protocol, wait)
>>   File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line
>> 64, in launch
>>     jobId = _launchRemote(protocol, wait)
>>   File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line
>> 164, in _launchRemote
>>     raise Exception("** Couldn't parse ouput: %s" % redStr(out))
>> Exception: ** Couldn't parse ouput: [31m
>> Scipion v1.1 (2017-06-14) Balbino
>>
>> [0m
>>
>>
>>
>> This email message and any attachments are confidential and intended for
>> use by the addressee(s) only. If you are not the intended recipient, please
>> notify me immediately by replying to this message, and destroy all copies
>> of this message and any attachments. Thank you.
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> notify me immediately by replying to this message, and destroy all copies
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Re: [scipion-users] problem using queuing system

[Gary S. <gar...@vr...>]

This is what a normal qsub does when you submit a script to UGE...

$ qsub busy.sh
Your job 6836 ("bz") has been submitted
$

From: Jose Miguel de la Rosa Trevin <del...@gm...<mailto:del...@gm...>>
Date: Tuesday, September 12, 2017 at 4:34 PM
To: Vertex <gar...@vr...<mailto:gar...@vr...>>
Cc: "sci...@li...<mailto:sci...@li...>" <sci...@li...<mailto:sci...@li...>>
Subject: Re: [scipion-users] problem using queuing system

Hi Gary,

This error is because Scipion is trying to parse the output from the submission command. It tries to parse a number (the job id) from the output. Can you share the output of a successful submission command to the queue? This could give us a hint about the issue.

Best,
Jose Miguel



On Sep 12, 2017 8:53 PM, "Gary Smith" <gar...@vr...<mailto:gar...@vr...>> wrote:
I'm trying to get Scipion-1.1 running with our Univa Grid Engine setup (aka. SGE).  Scipion appears to be failing to use the launch protocol remotely, even though this works fine outside of Scipion.  Has anyone seen errors like this?

Error during EXECUTE: ** Couldn't parse ouput: [31m
Scipion v1.1 (2017-06-14) Balbino

[0m

Traceback:
Traceback (most recent call last):
  File "/cluster/app/scipion/1.1/pyworkflow/gui/form.py", line 1710, in _close
    message = self.callback(self.protocol, onlySave)
  File "/cluster/app/scipion/1.1/pyworkflow/gui/project/viewprotocols.py", line 1662, in _executeSaveProtocol
    self.project.launchProtocol(prot)
  File "/cluster/app/scipion/1.1/pyworkflow/project.py", line 417, in launchProtocol
    pwprot.launch(protocol, wait)
  File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line 64, in launch
    jobId = _launchRemote(protocol, wait)
  File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line 164, in _launchRemote
    raise Exception("** Couldn't parse ouput: %s" % redStr(out))
Exception: ** Couldn't parse ouput: [31m
Scipion v1.1 (2017-06-14) Balbino

[0m



This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

Re: [scipion-users] problem using queuing system

[Jose M. de la R. T. <del...@gm...>]

Hi Gary,

This error is because Scipion is trying to parse the output from the
submission command. It tries to parse a number (the job id) from the
output. Can you share the output of a successful submission command to the
queue? This could give us a hint about the issue.

Best,
Jose Miguel



On Sep 12, 2017 8:53 PM, "Gary Smith" <gar...@vr...> wrote:

> I'm trying to get Scipion-1.1 running with our Univa Grid Engine setup
> (aka. SGE).  Scipion appears to be failing to use the launch protocol
> remotely, even though this works fine outside of Scipion.  Has anyone seen
> errors like this?
>
> Error during EXECUTE: ** Couldn't parse ouput: [31m
> Scipion v1.1 (2017-06-14) Balbino
>
> [0m
>
> Traceback:
> Traceback (most recent call last):
>   File "/cluster/app/scipion/1.1/pyworkflow/gui/form.py", line 1710, in
> _close
>     message = self.callback(self.protocol, onlySave)
>   File "/cluster/app/scipion/1.1/pyworkflow/gui/project/viewprotocols.py",
> line 1662, in _executeSaveProtocol
>     self.project.launchProtocol(prot)
>   File "/cluster/app/scipion/1.1/pyworkflow/project.py", line 417, in
> launchProtocol
>     pwprot.launch(protocol, wait)
>   File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line 64,
> in launch
>     jobId = _launchRemote(protocol, wait)
>   File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line
> 164, in _launchRemote
>     raise Exception("** Couldn't parse ouput: %s" % redStr(out))
> Exception: ** Couldn't parse ouput: [31m
> Scipion v1.1 (2017-06-14) Balbino
>
> [0m
>
>
>
> This email message and any attachments are confidential and intended for
> use by the addressee(s) only. If you are not the intended recipient, please
> notify me immediately by replying to this message, and destroy all copies
> of this message and any attachments. Thank you.
>
> ------------------------------------------------------------
> ------------------
> 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
>
>

[scipion-users] problem using queuing system

[Gary S. <gar...@vr...>]

I'm trying to get Scipion-1.1 running with our Univa Grid Engine setup (aka. SGE).  Scipion appears to be failing to use the launch protocol remotely, even though this works fine outside of Scipion.  Has anyone seen errors like this?

Error during EXECUTE: ** Couldn't parse ouput: [31m
Scipion v1.1 (2017-06-14) Balbino

[0m

Traceback:
Traceback (most recent call last):
  File "/cluster/app/scipion/1.1/pyworkflow/gui/form.py", line 1710, in _close
    message = self.callback(self.protocol, onlySave)
  File "/cluster/app/scipion/1.1/pyworkflow/gui/project/viewprotocols.py", line 1662, in _executeSaveProtocol
    self.project.launchProtocol(prot)
  File "/cluster/app/scipion/1.1/pyworkflow/project.py", line 417, in launchProtocol
    pwprot.launch(protocol, wait)
  File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line 64, in launch
    jobId = _launchRemote(protocol, wait)
  File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line 164, in _launchRemote
    raise Exception("** Couldn't parse ouput: %s" % redStr(out))
Exception: ** Couldn't parse ouput: [31m
Scipion v1.1 (2017-06-14) Balbino

[0m



This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

Re: [scipion-users] relion 3D_auto-refine

[Grigory S. <sha...@gm...>]

Hello Dmitry,

are you using release-1.1.1 branch from git? If you do movie processing in
Relion, inputs are movie particles (extracted using a separate protocol)
and a completed 3d auto-refine run with normal particles. Is this the case?
This error could happen only if your normal particles after relion
auto-refine 3d run do not have any shift information...

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...

On Thu, Sep 7, 2017 at 2:08 PM, D.A. Semchonok <sem...@gm...> wrote:

> Dear colleagues,
>
> I have a new issue running the relion 3d auto refinement -
>
> so
> - the input are the movies;
> - *Select previous run* the result of relion 3d auto-refine (with stacked
> frames)
>
>
>
> the error
>
> Converting set from 'Runs/032578_XmippProtExtractMovieParticles/movie_particles.sqlite'
> into 'Runs/032753_ProtRelionRefine3D/movie_particles.star'
> 00081:   Traceback (most recent call last):
> 00082:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py",
> line 182, in run
> 00083:       self._run()
> 00084:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py",
> line 228, in _run
> 00085:       resultFiles = self._runFunc()
> 00086:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py",
> line 224, in _runFunc
> 00087:       return self._func(*self._args)
> 00088:     File "/home/p260888/scipion/pyworkflow/em/packages/relion/protocol_base.py",
> line 805, in convertInputStep
> 00089:       mdAux.copyColumn(md.RLN_ORIENT_ORIGIN_X_PRIOR,
> md.RLN_ORIENT_ORIGIN_X)
> 00090:   XmippError: Source label: 'rlnOriginX' doesn't exist on metadata
> 00091:   Protocol failed: Source label: 'rlnOriginX' doesn't exist on
> metadata
> 00092:   FAILED: convertInputStep, step 1
> 00093:     2017-09-07 14:57:39.324748
> 00094:   ------------------- PROTOCOL FAILED (DONE 1/3)
>
>
> Suggestions?
>
> Thank you!
>
> Sincerely,
> Dmitry
>
> ------------------------------------------------------------
> ------------------
> 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
>
>

[scipion-users] relion 3D_auto-refine

[D.A. S. <sem...@gm...>]

Dear colleagues,

I have a new issue running the relion 3d auto refinement -

so
- the input are the movies;
- Select previous run the result of relion 3d auto-refine (with stacked 
frames)



the error

Converting set from 
'Runs/032578_XmippProtExtractMovieParticles/movie_particles.sqlite' into 
'Runs/032753_ProtRelionRefine3D/movie_particles.star'
00081:   Traceback (most recent call last):
00082:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py", 
line 182, in run
00083:       self._run()
00084:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py", 
line 228, in _run
00085:       resultFiles = self._runFunc()
00086:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py", 
line 224, in _runFunc
00087:       return self._func(*self._args)
00088:     File 
"/home/p260888/scipion/pyworkflow/em/packages/relion/protocol_base.py", 
line 805, in convertInputStep
00089:       mdAux.copyColumn(md.RLN_ORIENT_ORIGIN_X_PRIOR, 
md.RLN_ORIENT_ORIGIN_X)
00090:   XmippError: Source label: 'rlnOriginX' doesn't exist on 
metadata
00091:   Protocol failed: Source label: 'rlnOriginX' doesn't exist on 
metadata
00092:   FAILED: convertInputStep, step 1
00093:     2017-09-07 14:57:39.324748
00094:   ------------------- PROTOCOL FAILED (DONE 1/3)


Suggestions?

Thank you!

Sincerely,
Dmitry

[scipion-users] xmipp3 - extract movie particles

[D.A. S. <sem...@gm...>]

Dear colleagues,

When I execute the protocol xmipp3 - extract movie particles shall I 
enable the option Apply movie alignment to extract?

I want to do the particle polishing  after

sincerely,
Dmitry

Re: [scipion-users] error in installation

[Jose M. de la R. T. <del...@gm...>]

Hi,

I think that you have download the binary installation of Scipion...and
then you are forgetting
to add the '--no-xmipp' flag when running './scipion install EM-package-X'.
Please try to download
again and use the '--no-xmipp' flag to see if it works in that way.

Best,
Jose Miguel


On Mon, Aug 28, 2017 at 9:33 AM, abhisek Mondal <abh...@gm...>
wrote:

> Hi,
> I was recently trying to install scipion package but hitting an error
> every time. "./scipion install" command yields following error:
>
> scons: *** [software/em/xmipp/external/imagej/ij.jar] Source
> `software/em/xmipp/external/imagej.tgz' not found, needed by target
> `software/em/xmipp/external/imagej/ij.jar'.
>
> Seems imageJ is not available. Is there any way to overcome this issue ?
> Some advice regarding the same will be highly appreciated.
>
> Thank you.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
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