Hi Ross,
my last cuda problem was when simulating HCV.
Now I want to simulate HIV again (as I did before on GPU, but without
restraints) and face the following error:
| New format PARM file being parsed.
| Version = 1.000 Date = 08/19/11 Time = 16:50:58
./eq1.sh: line 42: 6664 Segmentation fault ${pmemd_cmd} -O -i eq1.in -o
eq1.out -p $top -c min.rst -r eq1.rst -x eq1.netcdf -ref min.rst
./eq2.sh: line 37: 6666 Segmentation fault ${pmemd_cmd} -O -i eq2.in -o
eq2.out -p $top -c eq1.rst -r eq2.rst -x eq2.netcdf -ref eq1.rst
At line 111 of file inpcrd_dat.f90 (unit = 9, file = 'eq2.rst')
Fortran runtime error: End of file
./eq3.sh: line 30: eq3.rst: File or directory not found
STOP PMEMD Terminated Abnormally!
Again, this works on CPU,
ah, and the infile is
equilibrate water and hydrogens (NVT)
&cntrl
ig=1,
irest=0,ntx=1,
nstlim=1000,dt=0.002,
temp0=300.0,ntt=1,tautp=1.0,
ntc=2,ntf=2,
cut=9,
ntpr=500,ntwx=5,ntwv=0,ntwe=5,
ntb=1,
ntr=1
/
Group 1
50.0
FIND
* * M *
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 1 100000
END
END
I'm out till 10.9. for vacancy now.
Maybe that helps you bugfixing.
Cheers,
Olli
--
Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de
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Received on Fri Aug 19 2011 - 08:00:05 PDT
