[gmx-users] OpenSuse 12.1 + CUDA Installation Error
Carlos Bueno
cabb99 at gmail.com
Thu Jul 25 04:25:59 CEST 2013
To install the CUDA I first downloaded and installed the drivers for the
Nvidia cards. The command nvidia-smi doen't give me any problems
> nvidia-smi
Wed Jul 24 17:36:28 2013
+------------------------------------------------------+
| NVIDIA-SMI 4.310.44 Driver Version: 310.44 |
|-------------------------------+----------------------+----------------------+
| GPU Name | Bus-Id Disp. | Volatile Uncorr.
ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
M. |
|===============================+======================+======================|
| 0 GeForce GTX 670 | 0000:01:00.0 N/A |
N/A |
| 16% 57C N/A N/A / N/A | 3% 67MB / 2047MB | N/A
Default |
+-------------------------------+----------------------+----------------------+
| 1 GeForce GTX 670 | 0000:02:00.0 N/A |
N/A |
| 71% 82C N/A N/A / N/A | 8% 157MB / 2047MB | N/A
Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Compute processes: GPU
Memory |
| GPU PID Process name Usage
|
|=============================================================================|
| 0 Not Supported
|
| 1 Not Supported
|
+-----------------------------------------------------------------------------+
Then, I downloaded the CUDA5 release for OpenSuse 12.1 from this page
https://developer.nvidia.com/cuda-downloads
but didn't reinstall the driver because that would downgrade my driver.
Now the cuda lib is found in /usr/local/cuda
I added all the repositories and installed all you told me.
And that solved the problem for one of the computers
The others still have an error in make:
[ 55%] Building NVCC (Device) object
src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o
/home/cuda2/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(216):
error: identifier "nbnxn_alloc_t" is undefined
/home/cuda2/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(217):
error: identifier "nbnxn_free_t" is undefined
2 errors detected in the compilation of
"/tmp/tmpxft_000076ad_00000000-11_nbnxn_cuda.compute_20.cpp2.i".
CMake Error at CMakeFiles/nbnxn_cuda_generated_nbnxn_cuda.cu.o.cmake:256
(message):
Error generating file
/home/cuda2/Programas/gromacs-4.6.3/build/src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o
make[2]: *** [src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o]
Error 1
make[1]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/all] Error 2
make: *** [all] Error 2
Thank you very much
I appreciate your help
2013/7/24 Mirco Wahab <mirco.wahab at chemie.tu-freiberg.de>
> On 24.07.2013 04:08, Carlos Bueno wrote:
>
>> *Hi,*
>> *I keep getting errors when I try to install gromacs in OpenSuse 12.1.*
>> *I have installed cuda 5.0 and the nvidia cards. **I have tried with
>> different parameters for cmake:*
>>
>
> How did you install Cuda5? What did you install and how?
>
> I have one OpenSuSE 12.1 box that works as a cluster head
> and serves to gpu-clusters. Every software except the
> nvidia gpu driver is installed on this box for usage by
> the nodes.
>
> Installing a gpu-ready OpenSuSE 12.1 involves (for example, YMMD)
> * add community- and extra-repositories through yast/repositories,
> these involve (here):
> (a) included in yast/repositories (activate only)
> Packman Repository
> openSUSE BuildService - devel:languages:perl
> openSUSE BuildService - devel:languages:python
> Education
> science
> (b) extra (add manually or ba script)
> devel:/tools
> devel:/libraries:/c_c++
> devel:/gcc
> you can do the latter by script:
> #
> #!/bin/sh
>
> Uri[1]="http://download.**opensuse.org/repositories/**
> devel:/tools/openSUSE_12.1/<http://download.opensuse.org/repositories/devel:/tools/openSUSE_12.1/>"
> Name[1]="devel:/tools"
>
> Uri[2]="http://download.**opensuse.org/repositories/**
> devel:/libraries:/c_c++/**openSUSE_12.1/<http://download.opensuse.org/repositories/devel:/libraries:/c_c++/openSUSE_12.1/>"
> Name[2]="devel:/libraries:/c_**c++"
>
> Uri[3]="http://download.**opensuse.org/repositories/**
> devel:/gcc/openSUSE_12.1/<http://download.opensuse.org/repositories/devel:/gcc/openSUSE_12.1/>"
> Name[3]="devel:/gcc"
> #
> for i in 1 2 3; do
> zypper --gpg-auto-import-keys ar ${Uri[i]} ${Name[i]}
> zypper modifyrepo --refresh ${Name[i]}
> done
> #
>
> * install gcc 4.6 / g++ 4.6 through yast
> * install fftw 3.3.3 through yast, look for the following packages:
> gpuclu:~ # rpm -qa |grep fftw
> libfftw3-3-3.3.3-5.1.x86_64
> fftw3-devel-3.3.3-5.1.x86_64
> fftw3-3.3-18.1.3.x86_64
> fftw3-threads-3.3-18.1.3.x86_**64
> fftw3-threads-devel-3.3.3-5.1.**x86_64
> libfftw3_threads3-3.3.3-5.1.**x86_64
> * install blas-devel, lapack-devel, gsl-devel through yast
> * Important: remove everything Nvidia-related stuff through yast, reboot
> * download and install (compile) the gpu driver
> NVIDIA-Linux-x86_64-319.32.run
> check if it functions properly (after reboot)
> * download and install CUDA from Nvidia:
> cuda_5.0.35_linux_64_suse12.1-**1.run
>
> if everything works, the command
> nvidia-smi
> should display some meaningful output.
>
>
>
> my € 0.05
>
> M.
>
> --
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