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MD-Studio / cerise-mdstudio-das5

A specialisation of cerise for MDStudio and DAS5
Apache License 2.0
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DAS5 update #18

Closed felipeZ closed 6 years ago

felipeZ commented 6 years ago

CUDA has been updated breaking the current gromacs installation

LourensVeen commented 6 years ago

Ah right, because we're uploading binaries, right? Hmm. Having the install script compile is also not great though, takes a long time.

felipeZ commented 6 years ago

Actually the CUDA drivers has changed and probably we need to recompile. There is also another issue with the intel compiler. I'm waiting for the answer of the DAS5 administrators

felipeZ commented 6 years ago

The CUDA75 libraries has been eliminated. I will try to recompile using CUDA90

LourensVeen commented 6 years ago

I'm pretty sure I used GCC, not sure if Intel will be faster but it's worth a try I guess. Here are some notes I took when compiling Gromacs on DAS, maybe useful?

[lveen@fs0 ~]$ cd gromacs/
[lveen@fs0 gromacs]$ wget 'http://ftp.gromacs.org/pub/gromacs/gromacs-2016.tar.gz'
[lveen@fs0 gromacs]$ tar xf gromacs-2016.tar.gz
[lveen@fs0 gromacs]$ cd gromacs-2016/
[lveen@fs0 gromacs-2016]$ mkdir build
[lveen@fs0 gromacs-2016]$ cd build
[lveen@fs0 build]$ module load fftw3/openmpi/gcc/64/3.3.4
[lveen@fs0 build]$ module load cuda75/blas/7.5.18
[lveen@fs0 build]$ module load cuda75/fft/7.5.18
[lveen@fs0 build]$ module load cuda75/gdk/352.79
[lveen@fs0 build]$ module load cuda75/toolkit/7.5.18
[lveen@fs0 build]$ module load openmpi/gcc/64/1.10.1
[lveen@fs0 build]$ ccmake ..

Hit 'c' to configure
CMAKE_INSTALL_PREFIX=/home/lveen/opt/gromacs5
GMX_MPI=ON (will disable THREAD_MPI, but that's ok)
GMX_DEFAULT_SUFFIX=OFF
Hit 'c' to configure again, and another 'c' to enable generation
Hit 'g' to generate

[lveen@fs0 build]$ make -j 8
[lveen@fs0 build]$ make install
[lveen@fs0 build]$ . ~/opt/gromacs5/bin/GMXRC.bash

You'll need to tweak the directories at least I guess, and IIRC the GXMRC.bash it installs has hard coded paths in it, so you may have to adjust those to point to $HOME/.cerise/... instead of whichever prefix you used when compiling. And use $HOME, because it'll be in the user's home dir, not in yours :).

felipeZ commented 6 years ago

Thanks for the script and the hints! We can not used the intel compilers due to this issue, therefore I'm using GCC and CUDA90.