Dear Marcus,
I'm not aware of the ctf_runner making any directory, so I'm a bit in the
dark here. Did someone change your mpi installation? What does 'which
mpiexec' or 'which mpirun' say? Are they the same as the ones you used to
compile relion 'ldd `which relion_refine_mpi`'?
HTH,
S
> Dear all,
>
> I just want to give a small update in case some people still try to figure
> out an answer.
> The second and third error message are now obsolete (due to a silly typo
> and a corrupted image) and ctffind4 is running properly if I am using only
> 1 mpi. However, if I am using submit to queue and multiple mpi procs I
> still get the first error message
>
>
>
>
> [node6:10373] opal_os_dirpath_create: Error: Unable to create the
> sub-directory (/tmp/openmpi-sessions-marcus@node6_0/33622) of
> (/tmp/openmpi-sessions-marcus@node6_0/33622/0/6), mkdir failed [1]
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../orte/util/session_dir.c at line 106
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../orte/util/session_dir.c at line 399
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../../../orte/mca/ess/base/ess_base_std_orted.c at line 266
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../../../../orte/mca/rml/oob/rml_oob_send.c at line 104
> [node6:10373] [[33622,0],6] could not get route to [[INVALID],INVALID]
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../orte/util/show_help.c at line 627
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../../../../orte/mca/ess/env/ess_env_module.c at line 143
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../../../../orte/mca/rml/oob/rml_oob_send.c at line 104
> [node6:10373] [[33622,0],6] could not get route to [[INVALID],INVALID]
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../orte/util/show_help.c at line 627
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../orte/runtime/orte_init.c at line 128
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../../../../orte/mca/rml/oob/rml_oob_send.c at line 104
> [node6:10373] [[33622,0],6] could not get route to [[INVALID],INVALID]
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../orte/util/show_help.c at line 627
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../orte/orted/orted_main.c at line 358
> ........
>
> Marcus Fislage, PhD
>
> Howard Hughes Medical Institute (HHMI)
> Columbia University
> Department of Biochemistry and Biophysics
> Lab of Joachim Frank
> New York, NY
>
> Phone: 212.305.9524
> Fax: 212.305.9500
> ________________________________
> From: Collaborative Computational Project in Electron cryo-Microscopy
> [[log in to unmask]] on behalf of Fislage, Marcus
> [[log in to unmask]]
> Sent: Friday, December 12, 2014 12:51 PM
> To: [log in to unmask]
> Subject: [ccpem] Running ctffind4 under relion 1.3 (using multiple mpi)
>
> Dear all,
>
> Currently it seems that I am not able anymore to run ctffind (using
> multiple mpi) through relion. This is the case for ctffind4 and 3. I now
> receive the error message below. We had it running before on this cluster
> and I cannot figure out what should have changed since my previous
> attempt.
> I have writing permissions on /tmp.
>
> Executing: bash run_ctffind_submit.script &
> [node6:10373] opal_os_dirpath_create: Error: Unable to create the
> sub-directory (/tmp/openmpi-sessions-marcus@node6_0/33622) of
> (/tmp/openmpi-sessions-marcus@node6_0/33622/0/6), mkdir failed [1]
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../orte/util/session_dir.c at line 106
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../orte/util/session_dir.c at line 399
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../../../orte/mca/ess/base/ess_base_std_orted.c at line 266
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../../../../orte/mca/rml/oob/rml_oob_send.c at line 104
> [node6:10373] [[33622,0],6] could not get route to [[INVALID],INVALID]
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../orte/util/show_help.c at line 627
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../../../../orte/mca/ess/env/ess_env_module.c at line 143
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../../../../orte/mca/rml/oob/rml_oob_send.c at line 104
> [node6:10373] [[33622,0],6] could not get route to [[INVALID],INVALID]
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../orte/util/show_help.c at line 627
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../orte/runtime/orte_init.c at line 128
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../../../../orte/mca/rml/oob/rml_oob_send.c at line 104
> [node6:10373] [[33622,0],6] could not get route to [[INVALID],INVALID]
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> ../../orte/util/show_help.c at line 627
> [node6:10373] [[33622,0],6] ORTE_ERROR_LOG: Error in file
> ../../orte/orted/orted_main.c at line 358
> ........
>
>
>
> If I run ctffind4 through relion using one 1 mpi the program seems to run
> successfully in one data set until at the end he complains not to be able
> to read the last line of the last log file and then does not write out the
> new star file.
>
>
>
> ERROR: cannot find line with Cs[mm], HT[kV], etc values in
> mics/align_14dec01e_XXX_00015gr_00002sq_v01_00008hl_00001en.frames_ctffind3.log
> File: src/ctffind_runner.cpp line: 297
>
>
>
> In another it stops running immediately and I receive the following error
> message
>
>
>
> Executing: `which relion_run_ctffind` --i "all_mics.star" --o
> "all_mics_ctf.star" --ctfWin -1 --CS 2.26 --HT 300 --AmpCnst 0.1 --XMAG
> 39683 --DStep 5 --Box 128 --ResMin 50 --ResMax 7 --dFMin 5000 --dFMax
> 60000 --FStep 250 --dAst 0 --ctffind3_exe
> "../ctffind/ctffind-4.0.7-linux64/ctffind --old-schold-input" &
> forrtl: severe (24): end-of-file during read, unit 5, file
> /proc/13325/fd/0
> Image PC Routine Line Source
> ctffind 000000000159F1F6 Unknown Unknown
> Unknown
> ctffind 000000000177DF11 Unknown Unknown
> Unknown
> ctffind 0000000001776D88 userinputs_MP_get 606
> user_input.f90
> ctffind 0000000001743E54 ctffind_IP_main_ 269
> ctffind.f90
> ctffind 0000000001741114 MAIN__ 53
> ctffind.f90
> ctffind 0000000000400566 Unknown Unknown
> Unknown
> ctffind 00000000016C12EB Unknown Unknown
> Unknown
> ctffind 0000000000400429 Unknown Unknown
> Unknown
> forrtl: severe (24): end-of-file during read, unit 5, file
> /proc/13330/fd/0
> Image PC Routine Line Source
> .......
>
>
>
> It would be good to know if somebody (Sjors) has an idea what it going
> wrong here.
>
> Cheers
> Marcus
>
> Marcus Fislage, PhD
>
> Howard Hughes Medical Institute (HHMI)
> Columbia University
> Department of Biochemistry and Biophysics
> Lab of Joachim Frank
> New York, NY
>
> Phone: 212.305.9524
> Fax: 212.305.9500
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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