Dear Amber Users,
I tried to install Amber 16 on my computer;
- GeForce GTX480
- NVIDIA Driver Version = 375.39
- Cuda version 8.0
- gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0
I successfully complied and installed the program.
*./configure -cuda gnu*
Cleaning the src directories. This may take a few moments.
*Configure complete*
*source amber.sh*
*make install*
make[4]: Leaving directory
'/home/kanin/Softwares/AMBER16/amber16/src/pmemd/src'
make[3]: Leaving directory
'/home/kanin/Softwares/AMBER16/amber16/src/pmemd/src'
*Installation of pmemd.cuda complete*
make[2]: Leaving directory '/home/kanin/Softwares/AMBER16/amber16/src/pmemd'
make[1]: Leaving directory '/home/kanin/Softwares/AMBER16/amber16/src'
*make test *
However, during testing the programs I got several errors; for example,
cd cellulose/ && ./Run.cellulose_nvt_256_128_128 DPFP
/home/kanin/Softwares/AMBER16/amber16/include/netcdf.mod
*cudaMalloc GpuBuffer::Allocate failed out of memory*
*./Run.cellulose_nvt_256_128_128: Program error*
*Makefile:166: recipe for target 'test.pmemd.cuda.pme.big' failed*
*make[3]: [test.pmemd.cuda.pme.big] Error 1 (ignored)*
cd cellulose/ && ./Run.cellulose_nvt DPFP
/home/kanin/Softwares/AMBER16/amber16/include/netcdf.mod
cudaMalloc GpuBuffer::Allocate failed out of memory
./Run.cellulose_nvt: Program error
Makefile:166: recipe for target 'test.pmemd.cuda.pme.big' failed
make[3]: [test.pmemd.cuda.pme.big] Error 1 (ignored)
cd cellulose/ && ./Run.cellulose_npt DPFP
/home/kanin/Softwares/AMBER16/amber16/include/netcdf.mod
cudaMalloc GpuBuffer::Allocate failed out of memory
./Run.cellulose_npt: Program error
Makefile:166: recipe for target 'test.pmemd.cuda.pme.big' failed
make[3]: [test.pmemd.cuda.pme.big] Error 1 (ignored)
make[3]: Leaving directory '/home/kanin/Softwares/AMBER16/amber16/test/cuda'
make[2]: Leaving directory '/home/kanin/Softwares/AMBER16/amber16/test'
124 file comparisons passed
8 file comparisons failed
15 tests experienced errors
and when I checked the file.diff there are a big difference in the values;
for example,
471c471
< EKCMT = 8798.1084 VIRIAL = 19449.8548 VOLUME = 366869.6118
> EKCMT = 8793.6574 VIRIAL = 19292.8185 VOLUME = 366873.2544
475c475
< NSTEP = 40 TIME(PS) = 50.040 TEMP(K) = 2.27 PRESS = 40.2
> NSTEP = 40 TIME(PS) = 50.040 TEMP(K) = 2.11 PRESS = 32.6
476c476
< Etot = 19.4103 EKtot = 149.8506 EPtot = 137.3725
> Etot = 25.6525 EKtot = 139.3085 EPtot = 126.1566
477c477
< BOND = 19.8977 ANGLE = 38.3546 DIHED = 11.8730
> BOND = 20.3404 ANGLE = 36.5091 DIHED = 12.9929
478c478
< 1-4 NB = 6.2284 1-4 EEL = 12.2396 VDWAALS = 46.4874
> 1-4 NB = 7.9763 1-4 EEL = 12.9424 VDWAALS = 50.6061
479c479
< EELEC = 87.3490 EHBOND = 0. RESTRAINT = 170.2276
> EELEC = 79.7127 EHBOND = 0. RESTRAINT = 169.9625
480c480
< EAMBER (non-restraint) = -32.8551
> EAMBER (non-restraint) = -43.8060
481c481
< EKCMT = 23.0457 VIRIAL = 327.6438 VOLUME = 251.4357
> EKCMT = 30.6251 VIRIAL = 272.3865 VOLUME = 248.0353
I successfully installed AMBER16 by using the same compiler, same version
of NVIDIA driver, CUDA, and Ubuntu but on different GPUs; Tesla C2075,
Quadro 6000, and GeForce GTX 1080 without any problems. So I think, it
might be because of GTX480 or not. Any suggestions to solve this problems.
Thank you in advance.
Best Regards,
Kanin Wichapong
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Received on Mon Mar 20 2017 - 07:00:02 PDT
