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m-a-d-n-e-s-s / madness

Multiresolution Adaptive Numerical Environment for Scientific Simulation
GNU General Public License v2.0
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Applications crash without error msg if built/installed with anaconda present #483

Open hborchert opened 1 year ago

hborchert commented 1 year ago

Installing madness on machine with anaconda installed leads to cmake finding MPI_C/MPI_CXX in anaconda directory and resulting applications crashing upon start, need to deactivate anaconda (conda deactivate env) before installing/running madness applications.

kottmanj commented 1 year ago

As far as I recall it works when the development versions are installed (at least on linux):

conda install mkl-devel

What is the error message when the application crashes? Something like: "Intel MKL FATAL ERROR: Cannot load libmkl_avx512.so.1 or libmkl_def.so.1."?

robertjharrison commented 1 year ago

This issue was also a problem on SeaWulf since the main Python module loads all of anaconda including that annoying MPI.

On Mon, Jun 12, 2023 at 9:51 AM J. S. Kottmann @.***> wrote:

As far as I recall it works when the development versions are installed (at least on linux):

conda install mkl-devel

What is the error message when the application crashes? Something like: "Intel MKL FATAL ERROR: Cannot load libmkl_avx512.so.1 or libmkl_def.so.1."?

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hborchert commented 1 year ago

No error message (on macOS) at all, application just crashes before reading input with "zsh: abort moldft" for example.

kottmanj commented 1 year ago

I also confused MPI with MKL ... sorry for that. However, some issues might be related. I think I don't get the MPI problems in conda envs since I usually deactivate it. With MKL there are the following fixes, that might work as well with MPI:

export MKLROOT variable before cmake configuration (needs to be exported on runtime as well)

export MKLROOT=/opt/intel/mkl

path needs to be adapted, depending on where MKL is installed. On clusters it often works to reload the module after loading the anaconda module. Then it often resets the MKLROOT variable.

There is also MPI_ROOT (here with underscore as far as I know) that might do the same trick in this case -- although I assume MPI is more tricky. On clusters I would try to reload the MPI module and hope for the best.

Another way is to set the paths to mpicxx and mpicc manually

cmake -D MPI_C_COMPILER=/path/to/bin/mpicc -D MPI_CXX_COMPILER=/path/to/bin/mpicxx ....

And when running explicitly calling

/path/to/bin/mpirun -n 1 moldft