Dear Amber creators,
I am trying to run the following script, involving a production step of my simulation, on an hpc facility:
#!/bin/bash --login
#PBS -N S4F4_md
#PBS -l walltime=24:00:00
#PBS -l select=4
#PBS -j oe
#PBS -A e280-Croft
module load amber
cd /work/e280/e280/enxds6/SF4
aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md1.out -p SF4.prmtop -c S4F4_heat.rst -r S4F4_md1.rst -x S4F4_md1.mdcrd
aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md2.out -p SF4.prmtop -c S4F4_md1.rst -r S4F4_md2.rst -x S4F4_md2.mdcrd
aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md3.out -p SF4.prmtop -c S4F4_md2.rst -r S4F4_md3.rst -x S4F4_md3.mdcrd
aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md4.out -p SF4.prmtop -c S4F4_md3.rst -r S4F4_md4.rst -x S4F4_md4.mdcrd
aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md5.out -p SF4.prmtop -c S4F4_md4.rst -r S4F4_md5.rst -x S4F4_md5.mdcrd
echo "DONE"
but I receive the same error message:
ModuleCmd_Load.c(226):ERROR:105: Unable to locate a modulefile for 'null'
ModuleCmd_Load.c(226):ERROR:105: Unable to locate a modulefile for 'null'
partition error in shake on processor 2
this processor has atoms 13055 through 19568
atom 19568 is within this range
atom 19569 is not within this range !
Rank 2 [Tue Aug 18 14:22:06 2015] [c4-2c2s8n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
Rank 0 [Tue Aug 18 14:22:06 2015] [c4-2c2s8n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 #0 0xDD499D0x in DD499D_gfortran_backtrace in _gfortran_backtrace at backtrace.c:258
at backtrace.c:258
#1 0xDBBAB0 in _gfortrani_backtrace_handler at compile_options.c:129
#1 0xDBBAB0 in _gfortrani_backtrace_handler at compile_options.c:129
#2 0xE3C43F in system
#3 0xE3C3EB in raise at pt-raise.c:41
#4 0xE4C8E0 in abort at abort.c:92
#5 0xD03EE1 in MPID_Abort
#6 0xCE3ED2 in MPI_Abort
#2 0xE3C43F in system
#3 0xE3C3EB in raise at pt-raise.c:41
#7 0xCBF1B4 in pmpi_abort
#4 0xE4C8E0 in abort at abort.c:92
#8 0x56EBB8 in mexit_
#5 0xD03EE1 in MPID_Abort
#9 0x4D7DCF in shake_
#10 0x4C19AD in runmd_
#6 0xCE3ED2 in MPI_Abort
#11 0x47EE31 in sander_
#7 0xCBF1B4 in pmpi_abort
#12 0x4783D5 in MAIN__ at multisander.F90:0
#8 0x56EBB8 in mexit_
#9 0x4D7DCF in shake_
#10 0x4C19AD in runmd_
#11 0x47EE31 in sander_
#12 0x4783D5 in MAIN__ at multisander.F90:0
_pmiu_daemon(SIGCHLD): [NID 04003] [c4-2c2s8n3] [Tue Aug 18 14:22:07 2015] PE RANK 0 exit signal Aborted
[NID 04003] 2015-08-18 14:22:07 Apid 16936164: initiated application termination
Application 16936164 exit codes: 134
Application 16936164 exit signals: Killed
Application 16936164 resources: utime ~2s, stime ~5s, Rss ~122380, inblocks ~277489, outblocks ~171369
Error opening unit 30: File "S4F4_md1.rst" is missing or unreadable
Rank 0 [Tue Aug 18 14:22:15 2015] [c4-2c2s8n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0xDD499D in _gfortran_backtrace at backtrace.c:258
#1 0xDBBAB0 in _gfortrani_backtrace_handler at compile_options.c:129
#2 0xE3C43F in system
#3 0xE3C3EB in raise at pt-raise.c:41
#4 0xE4C8E0 in abort at abort.c:92
#5 0xD03EE1 in MPID_Abort
#6 0xCE3ED2 in MPI_Abort
#7 0xCBF1B4 in pmpi_abort
#8 0x56EBB8 in mexit_
#9 0x5518AC in amopen_
#10 0x5EFD7F in amoeba_check_newstyle_inpcrd_
#11 0x4FCE7B in load_ewald_info_
#12 0x4A644E in mdread1_
#13 0x47954E in sander_
#14 0x4783D5 in MAIN__ at multisander.F90:0
_pmiu_daemon(SIGCHLD): [NID 04003] [c4-2c2s8n3] [Tue Aug 18 14:22:16 2015] PE RANK 0 exit signal Aborted
[NID 04003] 2015-08-18 14:22:16 Apid 16936165: initiated application termination
Application 16936165 exit codes: 134
Application 16936165 exit signals: Killed
Application 16936165 resources: utime ~0s, stime ~4s, Rss ~12120, inblocks ~75764, outblocks ~171353
Error opening unit 30: File "S4F4_md2.rst" is missing or unreadable
Rank 0 [Tue Aug 18 14:22:21 2015] [c4-2c2s8n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0xDD499D in _gfortran_backtrace at backtrace.c:258
#1 0xDBBAB0 in _gfortrani_backtrace_handler at compile_options.c:129
#2 0xE3C43F in system
#3 0xE3C3EB in raise at pt-raise.c:41
#4 0xE4C8E0 in abort at abort.c:92
#5 0xD03EE1 in MPID_Abort
#6 0xCE3ED2 in MPI_Abort
#7 0xCBF1B4 in pmpi_abort
#8 0x56EBB8 in mexit_
#9 0x5518AC in amopen_
#10 0x5EFD7F in amoeba_check_newstyle_inpcrd_
#11 0x4FCE7B in load_ewald_info_
#12 0x4A644E in mdread1_
#13 0x47954E in sander_
#14 0x4783D5 in MAIN__ at multisander.F90:0
_pmiu_daemon(SIGCHLD): [NID 04003] [c4-2c2s8n3] [Tue Aug 18 14:22:21 2015] PE RANK 0 exit signal Aborted
[NID 04003] 2015-08-18 14:22:21 Apid 16936166: initiated application termination
Application 16936166 exit codes: 134
Application 16936166 exit signals: Killed
Application 16936166 resources: utime ~0s, stime ~4s, Rss ~12120, inblocks ~75764, outblocks ~171353
Error opening unit 30: File "S4F4_md3.rst" is missing or unreadable
Rank 0 [Tue Aug 18 14:22:26 2015] [c4-2c2s8n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0xDD499D in _gfortran_backtrace at backtrace.c:258
#1 0xDBBAB0 in _gfortrani_backtrace_handler at compile_options.c:129
#2 0xE3C43F in system
#3 0xE3C3EB in raise at pt-raise.c:41
#4 0xE4C8E0 in abort at abort.c:92
#5 0xD03EE1 in MPID_Abort
#6 0xCE3ED2 in MPI_Abort
#7 0xCBF1B4 in pmpi_abort
#8 0x56EBB8 in mexit_
#9 0x5518AC in amopen_
#10 0x5EFD7F in amoeba_check_newstyle_inpcrd_
#11 0x4FCE7B in load_ewald_info_
#12 0x4A644E in mdread1_
#13 0x47954E in sander_
#14 0x4783D5 in MAIN__ at multisander.F90:0
_pmiu_daemon(SIGCHLD): [NID 04003] [c4-2c2s8n3] [Tue Aug 18 14:22:27 2015] PE RANK 0 exit signal Aborted
[NID 04003] 2015-08-18 14:22:27 Apid 16936168: initiated application termination
Application 16936168 exit codes: 134
Application 16936168 exit signals: Killed
Application 16936168 resources: utime ~0s, stime ~4s, Rss ~12120, inblocks ~75764, outblocks ~171353
Error opening unit 30: File "S4F4_md4.rst" is missing or unreadable
Rank 0 [Tue Aug 18 14:22:29 2015] [c4-2c2s8n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0xDD499D in _gfortran_backtrace at backtrace.c:258
#1 0xDBBAB0 in _gfortrani_backtrace_handler at compile_options.c:129
#2 0xE3C43F in system
#3 0xE3C3EB in raise at pt-raise.c:41
#4 0xE4C8E0 in abort at abort.c:92
#5 0xD03EE1 in MPID_Abort
#6 0xCE3ED2 in MPI_Abort
#7 0xCBF1B4 in pmpi_abort
#8 0x56EBB8 in mexit_
#9 0x5518AC in amopen_
#10 0x5EFD7F in amoeba_check_newstyle_inpcrd_
#11 0x4FCE7B in load_ewald_info_
#12 0x4A644E in mdread1_
#13 0x47954E in sander_
#14 0x4783D5 in MAIN__ at multisander.F90:0
_pmiu_daemon(SIGCHLD): [NID 04003] [c4-2c2s8n3] [Tue Aug 18 14:22:29 2015] PE RANK 0 exit signal Aborted
[NID 04003] 2015-08-18 14:22:29 Apid 16936169: initiated application termination
Application 16936169 exit codes: 134
Application 16936169 exit signals: Killed
Application 16936169 resources: utime ~0s, stime ~4s, Rss ~12120, inblocks ~75764, outblocks ~171353
DONE
All the requested files are in the correct directory.
>From the helpdesk of the hpc said might be an error in the SF4.prmtop file, but they are not sure about it.
It is the first time I am trying tu run this simulation on a cluster, I previously ran (just the first sander.MPI command) it on my machine and it worked, but I want to repeat this simulation on a cluster.
Any suggestions about something I'm probably missing?
Best
Damiano
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Received on Tue Aug 18 2015 - 07:00:03 PDT
