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enhance Amber easyblock for AmberTools #2618

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enhance Amber easyblock for AmberTools #2618

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d3f85aa
updated amber EasyBlock to support FlexiBLAS, netCDF-Fortran, and GCC…
mboisson Nov 11, 2021
2b73068
disable tests for AmberTools
mboisson Nov 12, 2021
78aabf4
Update easybuild/easyblocks/a/amber.py
mboisson Nov 30, 2021
a63a985
merged upstream develop
mboisson Aug 31, 2022
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18 changes: 13 additions & 5 deletions easybuild/easyblocks/a/amber.py
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Original file line number Diff line number Diff line change
Expand Up @@ -162,15 +162,21 @@ def configure_step(self):
external_libs_list.append('fftw')
if get_software_root('netCDF'):
external_libs_list.append('netcdf')
if get_software_root('netCDF-Fortran'):
netcdf_fortran_root = get_software_root('netCDF-Fortran')
if netcdf_fortran_root:
external_libs_list.append('netcdf-fortran')
self.cfg.update('configopts', '-DNetCDF_INCLUDES=%s/include' % netcdf_fortran_root)
if get_software_root('zlib'):
external_libs_list.append('zlib')
if get_software_root('Boost'):
external_libs_list.append('boost')
if get_software_root('PnetCDF'):
external_libs_list.append('pnetcdf')

# Force to use BLAS and LAPACK from environment variables
self.cfg.update('configopts', '-DBLAS_LIBRARIES="%s"' % os.getenv('LIBBLAS'))
self.cfg.update('configopts', '-DLAPACK_LIBRARIES="%s"' % os.getenv('LIBLAPACK'))

# Force libs for available deps (see cmake/3rdPartyTools.cmake in Amber source for list of 3rd party libs)
# This provides an extra layer of checking but should already be handled by TRUST_SYSTEM_LIBS=TRUE
external_libs = ";".join(external_libs_list)
Expand All @@ -187,9 +193,11 @@ def configure_step(self):

# Amber recommend running the tests from the sources, rather than putting in installation dir
# due to size. We handle tests under the install step
self.cfg.update('configopts', '-DINSTALL_TESTS=FALSE')
if "-DINSTALL_TESTS=" not in self.cfg['configopts']:
self.cfg.update('configopts', '-DINSTALL_TESTS=FALSE')

self.cfg.update('configopts', '-DCOMPILER=AUTO')
if "-DCOMPILER=" not in self.cfg['configopts']:
self.cfg.update('configopts', '-DCOMPILER=AUTO')

# configure using cmake
super(EB_Amber, self).configure_step()
Expand Down Expand Up @@ -315,8 +323,8 @@ def install_step(self):

super(EB_Amber, self).install_step()

# Run the tests located in the build directory
if self.cfg['runtest']:
# Run the tests located in the build directory, only for Amber. Tests fail when building only AmberTools
if self.cfg['runtest'] and self.name == 'Amber':
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do all tests fail with AmberTools, or only some?
if not all tests fail, I think it's still useful to run them in combination with EB option --ignore-test-failure.

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I did not try to untangle the tests, but not all executables from Amber get created, and the tests assume that they are there.

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See #2604 (and easybuilders/easybuild-easyconfigs#14028) - it is trying to run the Amber test suite and not the AmberTools test suite. There were still some failures with the AmberTool test suite and I've not had the chance to investigate further.

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Yeah, we're doing the runtest part wrong. I think I have the correct stuff in my test-.eb but I got sidetracked and haven't had time to go back and revisit.
It should not matter if we build Amber or AmberTools the test part (CMake and old style) is written so that it only tests what is actually built, if we call it correctly. I checked with the devs on that.

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@akesandgren did you hear back from the Amber devs yet?

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They basically said what I said above, The CMake part should do the right thing when asked to run make test.
But I haven't had time to revisit this on my side...

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This still fails as of today. Can't build AmberTools without disabling tests.

pretestcommands = 'source %s/amber.sh && cd %s/test' % (self.installdir, self.builddir)

# serial tests
Expand Down