[gmx-users] 2016.3 build issues Cray/KNL/HPC system, hwloc

[Sedova, Ada A.]

Hi,


I'm trying to build 2016.3 on the new ornl KNL which is, also, a cray. I succeeded multiple times using Intel PrgEnv to get the cmake to finish without error, using:


make .. -DCMAKE_INSTALL_PREFIX=/ccs/home/adaa/gromacs-2016.3/Install -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_BUILD_HELP=OFF -DGMX_HWLOC=OFF -DGMX_SIMD=AVX_512_KNL -DGMX_FFT_LIBRARY=mkl -DGMX_OPENMP_MAX_THREADS=256 > 1.out 2> 2.out

and also, with the -DBUILD_SHARED_LIBS=OFF option as well. Some of these flags I got from this website from Intel:

https://software.intel.com/en-us/articles/recipe-building-and-running-gromacs-on-intel-processors

After having some trouble getting cmake to complete without error. This was while trying both GCC programming environment, and with/without fftw module loaded. No matter what library paths and include paths I gave, cmake was unable to find required libraries until I used mkl and Intel compiler/PrgEnv.

Now, when I try to make, it crashed while attempting several compile lines in share/template/CMakeFiles/template.dir/link.txt and src/programs/CMakeFiles/gmx.dir/link.txt. I manually removed the -lhwloc flag and was able to make it past 98% to 100%. Then I get bunch more errors regarding hwloc, which can't be fixed as easily.

I saw some threads regarding this:

https://redmine.gromacs.org/issues/1919#change-14889

and I was wondering if there is any way to disable hwloc in the build, or some other work around. The
-DGMX_HWLOC=OFF flag apparently does not do it. I was having some trouble with using dynamic libraries, and I think cray does not really like the use of static libraries, at least on this system.

Calling hwloc from the machine's home node returns an unknown command error.

Thanks,

Ada





Ada Sedova

Postdoctoral Research Associate

Scientific Computing Group, NCCS

Oak Ridge National Laboratory, Oak Ridge, TN