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irisdyoung avatar irisdyoung commented on June 28, 2024 1

Thanks Felix -- I can build the kokkos branch now.

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Trzs avatar Trzs commented on June 28, 2024

The kokkos library fails to build on Perlmutter due to conflicts between Conda and libssh. You will need to remove the Conda libssh and load the "evp-patch" module:

> pwd

/global/cfs/cdirs/m3562/users/vidyagan/p20231/alcc-recipes2/cctbx

> rm opt/mamba/envs/psana_env/lib/libssh.so.4
> module load evp-patch

If you don't have a activate.sh, you will then need to replicate it's behavior before restarting the build:

> source utilities.sh
> source opt/site/nersc_perlmutter.sh
> load-sysenv
> activate

> mk-cctbx cuda build

WARNING: running setup_perlmutter.sh or mk-cctbx hot update will re-download the conda libssh, you will need to remove/rename it again.

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irisdyoung avatar irisdyoung commented on June 28, 2024

Hmm, that gets me further but I'm hitting this now:

===============================================================================
Building kokkos with cmake
-------------------------------------------------------------------------------
NameError: name 'cxx_standard' is not defined:
  File "/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/build/SConstruct", line 26:
    SConscript("simtbx/SConscript")
  File "/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/opt/mamba/envs/psana_env/lib/python3.8/site-packages/SCons/Script/SConscript.py", line 654:
    return method(*args, **kw)
  File "/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/opt/mamba/envs/psana_env/lib/python3.8/site-packages/SCons/Script/SConscript.py", line 591:
    return _SConscript(self.fs, *files, **subst_kw)
  File "/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/opt/mamba/envs/psana_env/lib/python3.8/site-packages/SCons/Script/SConscript.py", line 280:
    exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals)
  File "/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/modules/cctbx_project/simtbx/SConscript", line 34:
    env_simtbx.SConscript("../kokkostbx/SConscript")
  File "/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/opt/mamba/envs/psana_env/lib/python3.8/site-packages/SCons/Script/SConscript.py", line 591:
    return _SConscript(self.fs, *files, **subst_kw)
  File "/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/opt/mamba/envs/psana_env/lib/python3.8/site-packages/SCons/Script/SConscript.py", line 280:
    exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals)
  File "/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/modules/cctbx_project/kokkostbx/SConscript", line 111:
    '-DCMAKE_CXX_STANDARD={}'.format(cxx_standard),
usr+sys time: 2.57 seconds
wall clock time: 34.26 seconds
Process failed with return code 2

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Trzs avatar Trzs commented on June 28, 2024

Ah, I broke this recently, sorry. The new commit should fix this problem

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irisdyoung avatar irisdyoung commented on June 28, 2024

Ok, now getting this error. My cctbx sources are on the diffbragg2kokkos branch btw, which I'm not sure is the correct one -- which branch were you recommending I build?

/pscratch/sd/i/iris/xfel_kokkos/alcc-recipes/cctbx/modules/cctbx_project/simtbx/diffBragg/src/diffBragg_ext.cpp:457:5: error: 'kokkos_init' was not declared in this scope
  457 |     kokkos_init.device_id = dev;
      |     ^~~~~~~~~~~
scons: *** [simtbx/diffBragg/src/diffBragg_ext.o] Error 1

(confirmed this works on master though, thanks!)

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Trzs avatar Trzs commented on June 28, 2024

You probably got the kokkos 4.0 version. For the moment you need to go back to 3.7:

  • in modules /kokkos run git checkout 3.7.01
  • delete build/lib/libkokkos.a and also libkokkos in module/kokkos and all build files (just check untracked files with git status)
  • build CCTBX with mk-cctbx cuda build

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