Hello,
I am trying to use Amber/12.0 to model the interactions between the protein
Hfq and the RNA bound to it. I am an undergraduate lab member working at
UT Austin using Stampede at TACC. I am currently having trouble with one
of my equilibration steps. The error first occurred when trying to perform
an NPT simulation, which makes believe there may be an error in the restart
file obtained from the NVT simulation that was ran one step earlier. The
line counts for the min.restrt and NVT.restrt files are 68679 and 137355
lines, respectively. The graduate student I work under informed me there
should be twice as many lines in the NVT.restrt file; however, it is three
lines short of double. Below, I have copy and pasted the latest output
file to show an example of the error.
\login4$ wc *restrt
68679 412064 5013433 min.restrt
137355 824121 10026872 NVT.restrt
Dumping batchrscript
#!/bin/bash
#SBATCH -J eq_4HT9_ion # job name
#SBATCH -o eq_4HT9_ion.o%j # output and error file name (%j expands
to jobID)
#SBATCH -n 256 # total number of mpi tasks requested
#SBATCH -p normal # queue (partition) -- normal, development, etc.
#SBATCH -t 24:00:00 # run time (hh:mm:ss) - 1.5 hours
#SBATCH --mail-user=kyler123.tacc.utexas.edu
#SBATCH --mail-type=begin # email me when the job starts
#SBATCH --mail-type=end # email me when the job finishes
#SBATCH -A ProteinSpectroscopy # choose project to charge
compute time
echo "Dumping batchrscript" >> `ls -t eq_4HT9_ion.o* | head -n 1`
cat eq.sh >> `ls -t eq_4HT9_ion.o* | head -n 1`
set -x
#/usr/bin/time -p ibrun sander.MPI \
# -i ./eq.minin \
# -p 4HT9_ion.prmtop \
# -c 4HT9_ion.inpcrd \
# -o min.mdout \
# -x min.mdcrd \
# -r min.restrt \
# -e min.mden \
# -inf min.mdinfo
#/usr/bin/time -p ibrun sander.MPI \
# -i ./eq.NVTin \
# -p 4HT9_ion.prmtop \
# -c min.restrt \
# -o NVT.mdout \
# -x NVT.mdcrd \
# -r NVT.restrt \
# -e NVT.mden \
# -inf NVT.mdinfo
/usr/bin/time -p ibrun sander.MPI \
-i ./eq.NPTin \
-p 4HT9_ion.prmtop \
-c NVT.restrt \
-o NPT.mdout \
-x NPT.mdcrd \
-r NPT.restrt \
-e NPT.mden \
-inf NPT.mdinfo
+ /usr/bin/time -p ibrun sander.MPI -i ./eq.NPTin -p 4HT9_ion.prmtop -c
NVT.restrt -o NPT.mdout -x NPT.mdcrd -r NPT.restrt -e NPT.mden -inf
NPT.mdinfo
TACC: Starting up job 1562601
TACC: Setting up parallel environment for MVAPICH2+mpispawn.
TACC: Starting parallel tasks...
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.MPI 00000000005C3295 Unknown Unknown Unknown
sander.MPI 00000000005B8B17 Unknown Unknown Unknown
sander.MPI 000000000054FEEA Unknown Unknown Unknown
sander.MPI 00000000008B6D88 Unknown Unknown Unknown
sander.MPI 0000000000513501 Unknown Unknown Unknown
sander.MPI 00000000004C6EE0 Unknown Unknown Unknown
sander.MPI 00000000004BCA19 Unknown Unknown Unknown
sander.MPI 000000000040FBFC Unknown Unknown Unknown
libc.so.6 00000036AF81ECDD Unknown Unknown Unknown
sander.MPI 000000000040FAF9 Unknown Unknown Unknown
[c553-902.stampede.tacc.utexas.edu:mpispawn_15][readline] Unexpected
End-Of-File on file descriptor 11. MPI process died?
[c553-902.stampede.tacc.utexas.edu:mpispawn_15][mtpmi_processops] Error
while reading PMI socket. MPI process died?
[c553-902.stampede.tacc.utexas.edu:mpispawn_15][child_handler] MPI process
(rank: 254, pid: 111812) exited with status 174
[c547-803.stampede.tacc.utexas.edu:mpispawn_3][read_size] Unexpected
End-Of-File on file descriptor 24. MPI process died?
[c547-803.stampede.tacc.utexas.edu:mpispawn_3][read_size] Unexpected
End-Of-File on file descriptor 24. MPI process died?
[c547-803.stampede.tacc.utexas.edu:mpispawn_3][handle_mt_peer] Error while
reading PMI socket. MPI process died?
[c547-203.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c547-203.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c547-203.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error while
reading PMI socket. MPI process died?
[c547-401.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c547-401.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c547-401.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error while
reading PMI socket. MPI process died?
[c551-702.stampede.tacc.utexas.edu:mpispawn_4][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c551-702.stampede.tacc.utexas.edu:mpispawn_4][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c551-702.stampede.tacc.utexas.edu:mpispawn_4][handle_mt_peer] Error while
reading PMI socket. MPI process died?
TACC: MPI job exited with code: 1
TACC: Shutdown complete. Exiting.
real 283.85
user 1.20
sys 0.24
Here is some additional information that may be useful in troubleshooting
my problem:
I started with a .pdb file of the protein and RNA and removed hydrogens,
waters, and ions. Water and ions were added back into the system by the
following code:
source ~/kevleap.ff12SB
logfile 4HT9.leaplog
x=loadpdb 4HT9_noH.pdb
check x
saveamberparm x 4HT9.prmtop 4HT9.inpcrd
addions2 x Mg+ 49
addions2 x K+ 88
addions2 x Na+ 2
addions2 x Cl- 0
check x
solvatebox x TIP3PBOX 20.0 1.0
check x
saveamberparm x 4HT9_ion.prmtop 4HT9_ion.inpcrd
savepdb x 4HT9_ions.pdb
quit
(43499 water residues were added to the system, and the additional ions
were calculated using known cellular concentrations)
Once new files were generated for the neutralized system, minimization and
NVT simulations were ran.
Please let me know if there is any additional information that would be
useful. I tried to include as much pertinent information as I could think
of—hopefully, this is not too lengthy. Thank you in advance for any advice
you can offer me!
Thanks,
Kyler Cook
Contreras Lab
Department of Chemical Engineering
The University of Texas at Austin
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Received on Mon Sep 09 2013 - 13:30:02 PDT
