[AMBER] MMPBSA.py.MPI Nmode problem

From: filip fratev <filipfratev.yahoo.com>
Date: Wed, 19 Jan 2011 14:26:53 -0800 (PST)

Hi all,
I installed MMPBSA.py.MPI according to the instructions and it works in a parallel mode with MMPBSA, but when trying to calculate the entropy contribution I always obtain this error (please see below the example with the Amber test provided):
I use the last versions of Mpich2 (shared) and mpi4py and python 2.6 on Suse 11.3.
Thank you in advance for your help!

MMPBSA.py.MPI being run on 4 processors
ptraj found! Using /home/fratev/amber11/exe/ptraj
sander found! Using /home/fratev/amber11/exe/sander
nmode program found! Using /home/fratev/amber11/exe/mmpbsa_py_nabnmode

Preparing trajectories with ptraj...
10 frames were read in and processed by ptraj for use in calculation.
Processing 10 frames with normal mode analysis.

Starting calculations


Starting nmode calculations...
  master thread is calculating 3 frames

  calculating complex for frame number 0
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpYzsbx7
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
  calculating receptor for frame number 0
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpZYwgy5
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
  calculating ligand for frame number 0
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpxlXSY5
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
  calculating complex for frame number 1
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpa24cl6
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
  calculating receptor for frame number 1
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpv8T0C6
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
  calculating ligand for frame number 1
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpsZhzo6
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
  calculating complex for frame number 2
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpIORZa9
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
  calculating receptor for frame number 2
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpF8jqx9
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
  calculating ligand for frame number 2
[cli_0]: Command cmd=put kvsname=kvs_25724_0 key=sharedFilename[0] value=/dev/shm/mpich_shar_tmpUuGfV9
 failed, reason='duplicate_keysharedFilename[0]'
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388).....:
MPID_Init(135)............: channel initialization failed
MPIDI_CH3_Init(38)........:
MPID_nem_init(196)........:
MPIDI_CH3I_Seg_commit(337): PMI_KVS_Put returned -1
[mpiexec.linux-3ykv] HYDU_sock_read (./utils/sock/sock.c:213): read errno (Input/output error)
[mpiexec.linux-3ykv] HYDU_sock_forward_stdio (./utils/sock/sock.c:377): read error
[mpiexec.linux-3ykv] HYDT_bscu_stdin_cb (./tools/bootstrap/utils/bscu_cb.c:63): stdin forwarding error
[mpiexec.linux-3ykv] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:76): callback returned error status
[mpiexec.linux-3ykv] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:84): error waiting for event
[mpiexec.linux-3ykv] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting for completion
[mpiexec.linux-3ykv] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:352): bootstrap server returned error waiting for completion
[mpiexec.linux-3ykv] main (./ui/mpich/mpiexec.c:302): process manager error waiting for completion


      

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Received on Wed Jan 19 2011 - 14:30:03 PST
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