[gmx-users] gromacs installation (2020&2019)

[Netaly Khazanov]

Thank you for trying to help me. I will take into account all your comments.

On Sun, Apr 26, 2020 at 6:18 PM lazaro monteserin <
lamonteserincastanedo at gmail.com> wrote:

> Hey Netaly, are you trying to install Gromacs 2019 and 2020 at the same
> time? If not a couple of things to keep in mind.  Be sure before installing
> Gromacs you have all the utilities that Gromacs use, compilers, etc and
> that their versions are supported. I saw you are trying to install it for
> GPU, for that you need to install first the cuda toolkit versión for your
> linux. Now if you are installing Gromacs in an Ubuntu virtual machine on
> windows this is going to be a big problem. So for this case my
> recommendation is install it without GPU. Follow the instructions for
> installation in the website. Should work perfectly. Kindly, Lazaro
>
> On Sun, Apr 26, 2020 at 12:07 PM Yu Du <ydu-sci at outlook.com> wrote:
>
> > Hi Netaly,
> >
> > Although I do not know the exact reason of the failure, after skimming
> > through your command, I think that you probably need to assign absolute
> > path to CMAKE_INSTALL_PREFIX and have access to the internet for
> > downloading REGRESSIONTEST and FFTW package.
> >
> > If you are new to GROMACS, I recommend installation from simple case,
> such
> > as only CPU no GPU. Only after successfully installing CPU only version
> > GROMACS, run to the next level CPU+GPU. This step-by-step installation
> > practice can give you a feeling of choosing CMake options.
> >
> > Cheers,
> >
> > Du, Yu
> > PhD Student,
> > Shanghai Institute of Organic Chemistry
> > 345 Ling Ling Rd., Shanghai, China.
> > Zip: 200032, Tel: (86) 021 5492 5275
> > ________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Netaly
> > Khazanov <netalyk at gmail.com>
> > Sent: Sunday, April 26, 2020 15:38
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: [gmx-users] gromacs installation (2020&2019)
> >
> > Dear All,
> > I am trying to install gromacs 2020 and 2019 versions on CentOS release
> > 6.10 (Final) linux system.
> > I passed throuht cmake compilation. Using command
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=on
> > -DCMAKE_INSTALL_PREFIX=gromacs2020
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3
> > -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc
> > -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
> > -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
> > I've used gcc 5 version (tried also 6 version)
> >
> > However, I am struggling through make execution :
> > in gromacs 2019 -
> >
> > [ 37%] Built target libgromacs_generated
> > [ 37%] Built target libgromacs_external
> > Scanning dependencies of target gpu_utilstest_cuda
> > [ 37%] Linking CXX shared library
> ../../../../lib/libgpu_utilstest_cuda.so
> > [ 37%] Built target gpu_utilstest_cuda
> >
> > in gromacs 2020-
> > [ 27%] Built target linearalgebra
> > [ 27%] Built target scanner
> > [ 27%] Built target tng_io_obj
> > [ 27%] Built target modularsimulator
> >
> > It just stuck on the line and doesn't continue to run.
> >
> > Any suggestions will be appreciated.
> > Thanks in advance.
> >
> >
> > --
> > Netaly
> > --
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-- 
Netaly