Tried the #!/bin/bash and the script ran, but with problems:
==============================================================
cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm_noshake.md -1 SPDP
netcdf.mod
unknown flag:
-gpu
usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -inf mdinfo -l logfile]
[-suffix output_files_suffix]
STOP PMEMD Terminated Abnormally!
cat: mdout.dhfr_charmm_pbc_noshake_md: No such file or directory
diffing mdout.dhfr_charmm_pbc_noshake_md.GPU_SPDP with
mdout.dhfr_charmm_pbc_noshake_md
file ddtmp.mdout.dhfr_charmm_pbc_noshake_md is short
PASSED
/bin/rm: cannot remove `mdout.dhfr_charmm_pbc_noshake_md': No such file or
directory
==============================================================
cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm_noshake.min -1 SPDP
netcdf.mod
unknown flag:
-gpu
usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -inf mdinfo -l logfile]
[-suffix output_files_suffix]
STOP PMEMD Terminated Abnormally!
cat: mdout.dhfr_charmm_pbc_noshake_min: No such file or directory
diffing mdout.dhfr_charmm_pbc_noshake_min.GPU_SPDP with
mdout.dhfr_charmm_pbc_noshake_min
file ddtmp.mdout.dhfr_charmm_pbc_noshake_min is short
PASSED
/bin/rm: cannot remove `mdout.dhfr_charmm_pbc_noshake_min': No such file or
directory
==============================================================
make[1]: Leaving directory `/usr/local/amber11/test/cuda'
45 file comparisons passed
9 file comparisons failed
0 tests experienced errors
Test log file saved as logs/test_amber_cuda/2010-07-19_16-33-38.log
Test diffs file saved as logs/test_amber_cuda/2010-07-19_16-33-38.diff
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Using the echo args line, the script does not output any values for $1 or
$2.
If I run:
./test_amber_cuda.sh 1 SPDP > test2.txt
the variables do show ( args % 1 % SPDP % ), but with the same errors as
above.
Also, I've been trying to complile the other examples in the
NVIDIA_GPU_Computing_SDK files and keep bumping into different errors, maybe
something with the cuda card is not right?
Things like:
make[1]: *** [obj/release/cmd_arg_reader.cpp_o] Error 1
make[1]: Leaving directory `/home/ros/NVIDIA_CUDA_SDK/common'
make: *** [lib/libcutil.so] Error 2
Thanks again!
Rodrigo.
2010/7/19 Bill Ross <ross.cgl.ucsf.edu>
> > >From the test_amber_cuda.sh
> >
> > if [ "$1" == "" ]; then
> > echo "Using default GPU_ID = -1"
> > GPU_ID=-1
> > else
> > GPU_ID=$1
> > 35 >>> fi
>
> > >> > [: 35: unexpected operator
>
> I can't reproduce this error using /bin/sh on the version of linux
> I am on. You could try debugging by adding as the 2nd line of the
> script:
>
> echo args % $1 % $2 %
>
> to see what $1 and $2 actually are.
>
> Did you try making the first line:
>
> #!/bin/bash
>
> ? Since bash is probably better than sh anyway and might just work.
>
> Bill
>
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>
>
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Received on Mon Jul 19 2010 - 15:00:03 PDT
