[scipion-users] problem with CL2D

[Valerie B. <val...@ib...>]

Dear all,

I have installed the latest Scipion version on a linux machine Welcome to Ubuntu 16.04.1 LTS (GNU/Linux 4.4.0-59-generic x86_64).
the install tests have run OK but I have recurrent problems with CL2D: 

at first it was looking for  libmpi.so.1 so I created a symbolic link :
lrwxrwxrwx   1 root root      12 janv. 17 17:25 libmpi.so.1 -> libmpi.so.12

Now it fails with the message below.

Can you help me fix this, please?

Best regards,
Valerie


00001:   RUNNING PROTOCOL -----------------
00002:         Scipion: v1.0.1
00003:      currentDir: /home/biou/ScipionUserData/projects/EX_LMNG
00004:      workingDir: Runs/001509_XmippProtCL2D
00005:         runMode: Restart
00006:             MPI: 2
00007:         threads: 1
00008:    Starting at step: 1
00009:    Running steps 
00010:   STARTED: convertInputStep, step 1
00011:     2017-01-18 10:28:06.919867
00012:   FINISHED: convertInputStep, step 1
00013:     2017-01-18 10:28:14.324241
00014:   STARTED: runJob, step 2
00015:     2017-01-18 10:28:14.436293
00016:   mpirun -np 2 -bynode  `which xmipp_mpi_classify_CL2D` -i Runs/001509_XmippProtCL2D/extra/images.xmd --odir Runs/001509_XmippProtCL2D/extra --oroot level --nref 20 --iter 10  --distance correlation --classicalMultiref --nref0 4
00017:   --------------------------------------------------------------------------
00018:   The following command line options and corresponding MCA parameter have
00019:   been deprecated and replaced as follows:
00020:   
00021:     Command line options:
00022:       Deprecated:  --bynode, -bynode
00023:       Replacement: --map-by node
00024:   
00025:     Equivalent MCA parameter:
00026:       Deprecated:  rmaps_base_bynode
00027:       Replacement: rmaps_base_mapping_policy=node
00028:   
00029:   The deprecated forms *will* disappear in a future version of Open MPI.
00030:   Please update to the new syntax.
00031:   --------------------------------------------------------------------------
00032:   --------------------------------------------------------------------------
00033:   A requested component was not found, or was unable to be opened.  This
00034:   means that this component is either not installed or is unable to be
00035:   used on your system (e.g., sometimes this means that shared libraries
00036:   that the component requires are unable to be found/loaded).  Note that
00037:   Open MPI stopped checking at the first component that it did not find.
00038:   
00039:   Host:      vblinux
00040:   Framework: ess
00041:   Component: pmi
00042:   --------------------------------------------------------------------------
00043:   --------------------------------------------------------------------------
00044:   A requested component was not found, or was unable to be opened.  This
00045:   means that this component is either not installed or is unable to be
00046:   used on your system (e.g., sometimes this means that shared libraries
00047:   that the component requires are unable to be found/loaded).  Note that
00048:   Open MPI stopped checking at the first component that it did not find.
00049:   
00050:   Host:      vblinux
00051:   Framework: ess
00052:   Component: pmi
00053:   --------------------------------------------------------------------------
00054:   [vblinux:02124] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129
00055:   [vblinux:02123] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129
00056:   --------------------------------------------------------------------------
00057:   It looks like orte_init failed for some reason; your parallel process is
00058:   likely to abort.  There are many reasons that a parallel process can
00059:   fail during orte_init; some of which are due to configuration or
00060:   environment problems.  This failure appears to be an internal failure;
00061:   here's some additional information (which may only be relevant to an
00062:   Open MPI developer):
00063:   
00064:     orte_ess_base_open failed
00065:     --> Returned value Not found (-13) instead of ORTE_SUCCESS
00066:   --------------------------------------------------------------------------
00067:   --------------------------------------------------------------------------
00068:   It looks like orte_init failed for some reason; your parallel process is
00069:   likely to abort.  There are many reasons that a parallel process can
00070:   fail during orte_init; some of which are due to configuration or
00071:   environment problems.  This failure appears to be an internal failure;
00072:   here's some additional information (which may only be relevant to an
00073:   Open MPI developer):
00074:   
00075:     orte_ess_base_open failed
00076:     --> Returned value Not found (-13) instead of ORTE_SUCCESS
00077:   --------------------------------------------------------------------------
00078:   *** An error occurred in MPI_Init
00079:   *** on a NULL communicator
00080:   *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
00081:   ***    and potentially your MPI job)
00082:   *** An error occurred in MPI_Init
00083:   *** on a NULL communicator
00084:   *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
00085:   ***    and potentially your MPI job)
00086:   --------------------------------------------------------------------------
00087:   It looks like MPI_INIT failed for some reason; your parallel process is
00088:   likely to abort.  There are many reasons that a parallel process can
00089:   fail during MPI_INIT; some of which are due to configuration or environment
00090:   problems.  This failure appears to be an internal failure; here's some
00091:   additional information (which may only be relevant to an Open MPI
00092:   developer):
00093:   
00094:     ompi_mpi_init: ompi_rte_init failed
00095:     --> Returned "Not found" (-13) instead of "Success" (0)
00096:   --------------------------------------------------------------------------
00097:   --------------------------------------------------------------------------
00098:   It looks like MPI_INIT failed for some reason; your parallel process is
00099:   likely to abort.  There are many reasons that a parallel process can
00100:   fail during MPI_INIT; some of which are due to configuration or environment
00101:   problems.  This failure appears to be an internal failure; here's some
00102:   additional information (which may only be relevant to an Open MPI
00103:   developer):
00104:   
00105:     ompi_mpi_init: ompi_rte_init failed
00106:     --> Returned "Not found" (-13) instead of "Success" (0)
00107:   --------------------------------------------------------------------------
00108:   [vblinux:2124] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
00109:   [vblinux:2123] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
00110:   -------------------------------------------------------
00111:   Primary job  terminated normally, but 1 process returned
00112:   a non-zero exit code.. Per user-direction, the job has been aborted.
00113:   -------------------------------------------------------
00114:   --------------------------------------------------------------------------
00115:   mpirun detected that one or more processes exited with non-zero status, thus causing
00116:   the job to be terminated. The first process to do so was:
00117:   
00118:     Process name: [[63772,1],0]
00119:     Exit code:    1
00120:   --------------------------------------------------------------------------
00121:   Traceback (most recent call last):
00122:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 167, in run
00123:       self._run()
00124:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 211, in _run
00125:       resultFiles = self._runFunc()
00126:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 207, in _runFunc
00127:       return self._func(*self._args)
00128:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 960, in runJob
00129:       self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
00130:     File "/usr/local/scipion/pyworkflow/protocol/executor.py", line 56, in runJob
00131:       env=env, cwd=cwd)
00132:     File "/usr/local/scipion/pyworkflow/utils/process.py", line 51, in runJob
00133:       return runCommand(command, env, cwd)
00134:     File "/usr/local/scipion/pyworkflow/utils/process.py", line 65, in runCommand
00135:       check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, env=env, cwd=cwd)
00136:     File "/usr/local/scipion/software/lib/python2.7/subprocess.py", line 540, in check_call
00137:       raise CalledProcessError(retcode, cmd)
00138:   CalledProcessError: Command 'mpirun -np 2 -bynode  `which xmipp_mpi_classify_CL2D` -i Runs/001509_XmippProtCL2D/extra/images.xmd --odir Runs/001509_XmippProtCL2D/extra --oroot level --nref 20 --iter 10  --distance correlation --classicalMultiref --nref0 4' returned non-zero exit status 1
00139:   Protocol failed: Command 'mpirun -np 2 -bynode  `which xmipp_mpi_classify_CL2D` -i Runs/001509_XmippProtCL2D/extra/images.xmd --odir Runs/001509_XmippProtCL2D/extra --oroot level --nref 20 --iter 10  --distance correlation --classicalMultiref --nref0 4' returned non-zero exit status 1
00140:   FAILED: runJob, step 2
00141:     2017-01-18 10:28:14.966673
00142:   Cleaning temporarly files....
00143:   ------------------- PROTOCOL FAILED (DONE 2/13)