Thank you!
I tried the make test.cuda with the following errors:
ros.cuda:/usr/local/amber11/test$ make test.cuda
./test_amber_cuda.sh
[: 35: unexpected operator
[: 42: unexpected operator
make[1]: Entering directory `/usr/local/amber11/test'
cd cuda && make -k test.pmemd.cuda GPU_ID= PREC_MODEL=
make[2]: Entering directory `/usr/local/amber11/test/cuda'
------------------------------------
Running CUDA Implicit solvent tests.
Precision Model =
GPU_ID =
------------------------------------
cd gb_ala3/ && ./Run.igb1_ntc1_min netcdf.mod
../../../exe/pmemd.cuda_: Command not found.
./Run.igb1_ntc1_min: Program error
make[2]: *** [test.pmemd.cuda.gb] Error 1
------------------------------------
Running CUDA Explicit solvent tests.
Precision Model =
GPU_ID =
------------------------------------
cd 4096wat/ && ./Run.pure_wat netcdf.mod
../../../exe/pmemd.cuda_: Command not found.
./Run.pure_wat: Program error
make[2]: *** [test.pmemd.cuda.pme] Error 1
make[2]: Target `test.pmemd.cuda' not remade because of errors.
make[2]: Leaving directory `/usr/local/amber11/test/cuda'
make[1]: *** [test.pmemd.cuda] Error 2
make[1]: Target `test.serial.cuda' not remade because of errors.
make[1]: Leaving directory `/usr/local/amber11/test'
0 file comparisons passed
0 file comparisons failed
7 tests experienced errors
Test log file saved as logs/test_amber_cuda/2010-07-19_13-31-25.log
No test diffs to save!
------------------------------------------------------------------------------------------------------------------
The command:
./test_amber_cuda.sh -1 SPDP
worked but the test where not running as expected, for example:
==============================================================
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
==============================================================
Although it says passed, I dont think it did anything. When I try to run a
simulation of my own, it just gets stuck and nothing shows in the output
file.
Any help would be great!
thank you!
Rodrigo.
2010/7/19 case <case.biomaps.rutgers.edu>
> On Mon, Jul 19, 2010, ros wrote:
>
> > I am trying to run pmemd.cuda (AMBER11, ubuntu 10.04) with an nvida
> GT240.
> > I installed the CUDA SDK and the latest card driver.
> > ros.cuda:/usr/local/amber11/test$ ./test_amber_cuda.sh
>
> Don't do this. You are not supposed to run test_amber_cuda.sh directly,
> but rather, you should type "make test.cuda"
> > [: 35: unexpected operator
> > [: 42: unexpected operator
> > cd cuda && make -k test.pmemd.cuda GPU_ID= PREC_MODEL=
>
> Your GPU_ID and PREC_MODEL are not being set: see the test_amber_cuda.sh
> file. The problem is the "unexpected operator" messages.
>
> You can try to change /bin/sh at the top of that script to /bin/bash, but
> I don't see the error in the script. Maybe someone on the list will have
> better eyeballs. If using bash doesn't work, then you will have run the
> script like this:
>
> ./test_amber_cuda.sh -1 SPDP
>
> ....dac
>
>
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>
>
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Received on Mon Jul 19 2010 - 12:00:03 PDT
