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fix AmberTools v20 easyconfig using intel/2020a toolchain #14028

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merged 7 commits into from
Oct 21, 2021
Merged

fix AmberTools v20 easyconfig using intel/2020a toolchain #14028

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339f035
fix AmberTools v20 easyconfig (WIP)
boegel Sep 17, 2021
77b79e8
add patch files for AmberTools 20
boegel Sep 21, 2021
33f18b4
Fix AmberTools build with intel compiler
branfosj Oct 14, 2021
76e4db6
fix typo in prebuildopts in AmberTools 20 easyconfig
boegel Oct 14, 2021
a009b8b
Merge pull request #83 from branfosj/at_icc
boegel Oct 14, 2021
cbc69bf
add xblas patch and flex & make deps
branfosj Oct 16, 2021
d0842d5
Merge pull request #84 from branfosj/at_review
boegel Oct 16, 2021
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29 changes: 22 additions & 7 deletions easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -19,26 +19,41 @@ sources = [{
'download_filename': local_download_credentials,
'filename': SOURCE_TAR_BZ2,
}]
patches = ['Amber-20_fix-hardcoding.patch']
patches = [
'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
'AmberTools-20_cmake-locate-netcdf.patch',
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'AmberTools-20_fix_xblas_missing_make_dependency.patch',
]
checksums = [
'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools-20.tar.bz2
'a71f1bd70bac8d5e25386d6db90e95874ad300b956ed5b5afbc8848b7c1e00dc', # Amber-20_fix-hardcoding.patch
# AmberTools-20_fix_missing_MPI_LIBRARY_error.patch'
'0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc',
'473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch
# AmberTools-20_fix_xblas_missing_make_dependency.patch
'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65'
]

builddependencies = [
('Bison', '3.5.3'),
('pkg-config', '0.29.2'),
('CMake', '3.16.4'),
('flex', '2.6.4'),
('make', '4.3'),
]
dependencies = [
('Python', '3.8.2'),
('SciPy-bundle', '2020.03', versionsuffix),
('matplotlib', '3.2.1', versionsuffix),
('netCDF', '4.7.4'),
('netCDF-Fortran', '4.5.2'),
('FFTW', '3.3.8'),
]

# fix linking to netCDF library: also requires linking to HDF5 & cURL libs, which in turns require others,
# all of which are indirect dependencies via netCDF
local_netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -liomp5 -lcurl -lssl -lcrypto -lz -lm -lpthread"
preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' AmberTools/src/cpptraj/configure && " % local_netcdf_libs
configopts = "-nosanderapi"
# pysander should link with icc and not gcc
prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' """
prebuildopts += "%(builddir)s/AmberTools/src/pysander/setup.py && "

# Tests use pmemd which is not part of AmberTools
runtest = False
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I think runtest = "test.serial" should avoid that.

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With runtest ="test.serial" I get lots of failures. Full log of the test section in the section below.

Lots of failure 
== 2021-10-18 09:24:42,496 run.py:233 INFO running cmd: source /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2/amber.sh && cd /dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test && make test 
== 2021-10-18 09:24:51,792 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd "source /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2/amber.sh && cd /dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test && make test" exited with exit code 2 and output:
./test_amber_clean.sh
./test_amber_clean.sh: line 1276: cd: cuda/remd: No such file or directory
make: [Makefile:1670: clean] Error 1 (ignored)
./test_amber_serial.sh
make[1]: Entering directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test'
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd nonper && ./Run.egb6
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.egb6:  Program error
make[1]: [Makefile:1068: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd 4096wat && ./Run.pure_wat
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pure_wat:  Program error
make[1]: [Makefile:1069: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd 4096wat && ./Run.pure_wat_nmr_temp_reg
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pure_wat_nmr_temp_reg:  Program error
make[1]: [Makefile:1070: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd 4096wat && ./Run.vrand
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.vrand:  Program error
make[1]: [Makefile:1071: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd 4096wat && ./Run.frcdmp
./Run.frcdmp: line 28: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.frcdmp: Program error
make[1]: [Makefile:1072: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd 4096wat_oct && ./Run.pure_wat_oct
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pure_wat_oct:  Program error
make[1]: [Makefile:1073: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd 4096wat && ./Run.pure_wat_fswitch
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pure_wat_fswitch:  Program error
make[1]: [Makefile:1074: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd 4096wat && ./Run.pure_wat_efield
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pure_wat_efield:  Program error
make[1]: [Makefile:1075: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd alp && ./Run.alp
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.alp:  Program error
make[1]: [Makefile:1076: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cytosine && ./Run.cytosine
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.cytosine:  Program error
make[1]: [Makefile:1077: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd dhfr && ./Run.dhfr
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr:  Program error
make[1]: [Makefile:1078: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd dhfr && ./Run.dhfr.min
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr.min:  Program error
make[1]: [Makefile:1079: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd dhfr && ./Run.dhfr.noshake
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr.noshake:  Program error
make[1]: [Makefile:1080: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd dhfr && ./Run.dhfr.bussi
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr.bussi:  Program error
make[1]: [Makefile:1081: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd dhfr && ./Run.dhfr_reweight
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr_reweight:  Program error
make[1]: [Makefile:1082: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd ff14ipq && ./Run.ff14ipq
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.ff14ipq:  Program error
make[1]: [Makefile:1083: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd variable_14 && ./Run.variable_14_ntb1
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.variable_14_ntb1:  Program error
make[1]: [Makefile:1084: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd variable_14 && ./Run.variable_14_igb1
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.variable_14_igb1:  Program error
make[1]: [Makefile:1085: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd trx && ./Run.trx
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.trx:  Program error
make[1]: [Makefile:1086: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd trx && ./Run.trx.cpln.pmemd
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.trx.cpln.pmemd:  Program error
make[1]: [Makefile:1087: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb_rna && ./Run.gbrna
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbrna:  Program error
make[1]: [Makefile:1088: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb_rna && ./Run.gbrna.min
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbrna.min:  Program error
make[1]: [Makefile:1089: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb_rna && ./Run.gbrna.ln
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbrna.ln:  Program error
make[1]: [Makefile:1090: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd circ_dna && ./Run.circdna
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.circdna:  Program error
make[1]: [Makefile:1091: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb2_trx && ./Run.trxox.nogbsa && ./Run.trxox.nogbsa prmtop_an
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.trxox.nogbsa:  Program error
make[1]: [Makefile:1092: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb7_trx && ./Run.trxox_md
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.trxox_md:  Program error
make[1]: [Makefile:1093: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb8_trx && ./Run.trxox
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.trxox:  Program error
make[1]: [Makefile:1094: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb8_trx && ./Run.trxox_md && ./Run.trxox_md prmtop_an
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.trxox_md:  Program error
make[1]: [Makefile:1095: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd mcwat && ./Run.mcwat
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.mcwat:  Program error
make[1]: [Makefile:1096: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd RAMD && ./Run.ramd
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.ramd:  Program error
make[1]: [Makefile:1097: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd ff19SB && ./Run.pmemd
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pmemd:  Program error
make[1]: [Makefile:1098: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gbneck2nu/1hji && ./Run.1hji_md
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.1hji_md:  Program error
make[1]: [Makefile:1099: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gbneck2nu/modified_nu/3p4a/ && ./Run.3p4a
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.3p4a:  Program error
make[1]: [Makefile:1100: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd alpb_trx && ./Run.trxox.nogbsa
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.trxox.nogbsa:  Program error
make[1]: [Makefile:1101: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gbsa_xfin && ./Run.gbsa1
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbsa1:  Program error
make[1]: [Makefile:1102: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gbsa_xfin && ./Run.gbsa3
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbsa3:  Program error
make[1]: [Makefile:1103: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd tip4p && ./Run.tip4p
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.tip4p:  Program error
make[1]: [Makefile:1104: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd tip4p && ./Run.tip4p_mcbar
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.tip4p_mcbar:  Program error
make[1]: [Makefile:1105: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd tip4p && ./Run.tip4p_nve
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.tip4p_nve:  Program error
make[1]: [Makefile:1106: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd tip5p && ./Run.tip5p
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.tip5p:  Program error
make[1]: [Makefile:1107: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd tip5p && ./Run.tip5p_nve
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.tip5p_nve:  Program error
make[1]: [Makefile:1108: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cnstph/implicit && ./Run.cnstph
./Run.cnstph: line 43: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.cnstph: Program error
make[1]: [Makefile:1109: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cnstph/explicit && ./Run.cnstph
./Run.cnstph: line 31: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.cnstph: Program error
make[1]: [Makefile:1110: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd phmd/implicit && ./Run.phmd
./Run.phmd: line 43: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.phmd: Program error
make[1]: [Makefile:1111: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cnste/implicit && ./Run.cnste
./Run.cnste: line 43: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.cnste: Program error
make[1]: [Makefile:1112: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cnste/explicit && ./Run.cnste
./Run.cnste: line 35: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.cnste: Program error
make[1]: [Makefile:1113: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cnstphe/implicit && ./Run.cnstphe
./Run.cnstphe: line 44: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.cnstphe: Program error
make[1]: [Makefile:1114: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cnstphe/explicit && ./Run.cnstphe
./Run.cnstphe: line 33: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.cnstphe: Program error
make[1]: [Makefile:1115: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cnstphe_merged/implicit && ./Run.cnstphe
./Run.cnstphe: line 44: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.cnstphe: Program error
make[1]: [Makefile:1116: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd cnstphe_merged/explicit && ./Run.cnstphe
./Run.cnstphe: line 32: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.cnstphe: Program error
make[1]: [Makefile:1117: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.min
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr_charmm.min:  Program error
make[1]: [Makefile:1118: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.md
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr_charmm.md:  Program error
make[1]: [Makefile:1119: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.md
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr_charmm.md:  Program error
make[1]: [Makefile:1120: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.min
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr_cmap_pbc_charmm_noshake.min:  Program error
make[1]: [Makefile:1121: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.md
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr_cmap_pbc_charmm_noshake.md:  Program error
make[1]: [Makefile:1122: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.min
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr_cmap_pbc_charmm.min:  Program error
make[1]: [Makefile:1123: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.md
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dhfr_cmap_pbc_charmm.md:  Program error
make[1]: [Makefile:1124: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gact_ips && ./Run.ips
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.ips:  Program (ignored) error
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd csurften && ./Run.csurften_z-dir
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.csurften_z-dir:  Program error
make[1]: [Makefile:1126: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd lj_12-6-4 && ./Run.12-6-4
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.12-6-4:  Program error
make[1]: [Makefile:1127: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd csurften && ./Run.csurften_z-dir_npt_3
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.csurften_z-dir_npt_3:  Program error
make[1]: [Makefile:1128: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd nmropt && make pmemd_compat
make[2]: Entering directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/nmropt'
cd gb/angle && ./Run.nmropt_1angle_gb
./Run.nmropt_1angle_gb: line 43: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.nmropt_1angle_gb: Program error
make[2]: [Makefile:13: pmemd_compat_gb] Error 1 (ignored)
cd gb/distance && ./Run.dist_gb
./Run.dist_gb: line 49: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.dist_gb: Program error
make[2]: [Makefile:14: pmemd_compat_gb] Error 1 (ignored)
cd gb/distance_COM && ./Run.distCOM_gb
./Run.distCOM_gb: line 49: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.distCOM_gb: Program error
make[2]: [Makefile:15: pmemd_compat_gb] Error 1 (ignored)
cd gb/jar_distance && ./Run.jar_gb
./Run.jar_gb: line 47: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.jar_gb: Program error
make[2]: [Makefile:16: pmemd_compat_gb] Error 1 (ignored)
cd gb/jar_distance_COM && ./Run.jar_gb
./Run.jar_gb: line 48: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.jar_gb: Program error
make[2]: [Makefile:17: pmemd_compat_gb] Error 1 (ignored)
cd gb/jar_torsion && ./Run.jar_torsion
./Run.jar_torsion: line 45: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.jar_torsion: Program error
make[2]: [Makefile:18: pmemd_compat_gb] Error 1 (ignored)
cd gb/nmropt_1_torsion && ./Run.nmropt_1_torsion
./Run.nmropt_1_torsion: line 46: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.nmropt_1_torsion: Program error
make[2]: [Makefile:19: pmemd_compat_gb] Error 1 (ignored)
cd gb/tautp && ./Run.nmropt_1tautp_gb
./Run.nmropt_1tautp_gb: line 37: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.nmropt_1tautp_gb: Program error
make[2]: [Makefile:20: pmemd_compat_gb] Error 1 (ignored)
cd gb/temp && ./Run.nmropt_1temp_gb
./Run.nmropt_1temp_gb: line 37: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.nmropt_1temp_gb: Program error
make[2]: [Makefile:21: pmemd_compat_gb] Error 1 (ignored)
cd gb/angle_torsion_com/ && ./Run.angdihCOM_gb
./Run.angdihCOM_gb: line 64: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.angdihCOM_gb: Program error
make[2]: [Makefile:22: pmemd_compat_gb] Error 1 (ignored)
cd pme/angle && ./Run.nmropt_1angle_pbc
./Run.nmropt_1angle_pbc: line 44: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.nmropt_1angle_pbc: Program error
make[2]: [Makefile:34: pmemd_compat_pme] Error 1 (ignored)
cd pme/distance && ./Run.dist_pbc
./Run.dist_pbc: line 52: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.dist_pbc: Program error
make[2]: [Makefile:35: pmemd_compat_pme] Error 1 (ignored)
cd pme/distance_COM && ./Run.distCOM_pbc
./Run.distCOM_pbc: line 53: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.distCOM_pbc: Program error
make[2]: [Makefile:36: pmemd_compat_pme] Error 1 (ignored)
cd pme/jar_torsion && ./Run.jar_torsion
./Run.jar_torsion: line 48: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.jar_torsion: Program error
make[2]: [Makefile:37: pmemd_compat_pme] Error 1 (ignored)
cd pme/jar_distance && ./Run.jar_pbc
./Run.jar_pbc: line 52: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.jar_pbc: Program error
make[2]: [Makefile:38: pmemd_compat_pme] Error 1 (ignored)
cd pme/jar_distance_COM && ./Run.jar_pbc
./Run.jar_pbc: line 52: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.jar_pbc: Program error
make[2]: [Makefile:39: pmemd_compat_pme] Error 1 (ignored)
cd pme/nmropt_1_torsion && ./Run.nmropt_1_torsion
./Run.nmropt_1_torsion: line 49: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.nmropt_1_torsion: Program error
make[2]: [Makefile:40: pmemd_compat_pme] Error 1 (ignored)
cd pme/tautp && ./Run.nmropt_1tautp_pbc
./Run.nmropt_1tautp_pbc: line 39: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.nmropt_1tautp_pbc: Program error
make[2]: [Makefile:41: pmemd_compat_pme] Error 1 (ignored)
cd pme/temp && ./Run.nmropt_1temp_pbc
./Run.nmropt_1temp_pbc: line 39: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.nmropt_1temp_pbc: Program error
make[2]: [Makefile:42: pmemd_compat_pme] Error 1 (ignored)
cd pme/angle_torsion_com/ && ./Run.angdihCOM
./Run.angdihCOM: line 68: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.angdihCOM: Program error
make[2]: [Makefile:43: pmemd_compat_pme] Error 1 (ignored)
make[2]: Leaving directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/nmropt'
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd rdc && ./Run.nmr
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.nmr:  Program error
make[1]: [Makefile:1130: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd netcdf && make -k test OPT=yes
make[2]: Entering directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/netcdf'
  Netcdf MD Restart Write Test
./runmd.sh: line 32: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./runmd.sh: Program error
make[2]: [Makefile:6: mdrstwrite] Error 1 (ignored)
  Netcdf Minimization Restart Write Test
./runmin.sh: line 28: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./runmin.sh: Program error
make[2]: [Makefile:9: minrstwrite] Error 1 (ignored)
  Restrained MD with netcdf Restart Reference Coords Test
./runmd.sh: line 34: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./runmd.sh: Program error
make[2]: [Makefile:12: ncrefmd] Error 1 (ignored)
  Netcdf MD restart read test, ntx=5
./runmd.sh: line 35: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./runmd.sh: Program error
make[2]: [Makefile:15: ntx5] Error 1 (ignored)
  Netcdf MD restart read test, ntx=1
./runmd.sh: line 35: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./runmd.sh: Program error
make[2]: [Makefile:18: ntx1] Error 1 (ignored)
make[2]: Leaving directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/netcdf'
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd baroscalingdir && ./Run.baroscalingdir_z-dir
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.baroscalingdir_z-dir:  Program error
make[1]: [Makefile:1132: test.serial.pmemd.basic] Error 1 (ignored)
make[2]: Entering directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test'
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd xray/2wcu && ./Run.2wcu
/usr/bin/bash: line 0: cd: xray/2wcu: No such file or directory
make[2]: [Makefile:1157: test.serial.pmemd.xray] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd xray/480d && ./Run.480d
/usr/bin/bash: line 0: cd: xray/480d: No such file or directory
make[2]: [Makefile:1158: test.serial.pmemd.xray] Error 1 (ignored)
make[2]: Leaving directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test'
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd velocity_write && ./Run.vel1
./Run.vel1: line 39: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.vel1: Program error
make[1]: [Makefile:1134: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd velocity_write && ./Run.vel2
./Run.vel2: line 25: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.vel2: line 46: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: No such file or directory
./Run.vel2: Program error
make[1]: [Makefile:1135: test.serial.pmemd.basic] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/gasphase && ./Run.gasphase
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gasphase:  Program error
make[1]: [Makefile:1161: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/campTI && ./Run.campTI
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.campTI:  Program error
make[1]: [Makefile:1162: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/pheMTI && ./Run.0
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.0:  Program error
make[1]: [Makefile:1163: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/pheMTI && ./Run.1
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.1:  Program error
make[1]: [Makefile:1164: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/pheMTI && ./Run.lambda0
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.lambda0:  Program error
make[1]: [Makefile:1165: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/pheMTI && ./Run.lambda1
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.lambda1:  Program error
make[1]: [Makefile:1166: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/sodium && ./Run.sodium
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.sodium:  Program error
make[1]: [Makefile:1167: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/ti_ggcc && ./Run.test1
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.test1:  Program error
make[1]: [Makefile:1168: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/ti_ggcc && ./Run.test2
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.test2:  Program error
make[1]: [Makefile:1169: test.serial.pmemd.TI] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd pmemdTI/softcore && ./Run_sc
Running the Softcore potential tests
==============================================================
  Minimization test
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.min:  Program error
 
  Protein-Ligand complex test
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.complex:  Program error
 
==============================================================
  Solvation free energy test
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.toluene:  Program error
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.toluene2:  Program error
 
==============================================================
  Dynamic lambda test
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.dynlmb:  Program error
 
==============================================================
  Restrained complex test
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.complex_rst:  Program error
 
==============================================================
  Using softcore electrostatics
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.ethanol:  Program error
 
==============================================================
Soft core test suite complete
 
==============================================================
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gact_ips && ./Run.ips_sgld
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.ips_sgld:  Program error
make[1]: [Makefile:1219: test.serial.pmemd.sgld] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gact_ips && ./Run.ips_sgldfp
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.ips_sgldfp:  Program (ignored) error
make[1]: [Makefile:1220: test.serial.pmemd.sgld] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gact_ips && ./Run.ips_sgldg
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.ips_sgldg:  Program error
make[1]: [Makefile:1221: test.serial.pmemd.sgld] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gact_ips && ./Run.ips_sgmdg
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.ips_sgmdg:  Program (ignored) error
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb_rna && ./Run.gbrna.sgld
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbrna.sgld:  Program error
make[1]: [Makefile:1223: test.serial.pmemd.sgld] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb_rna && ./Run.gbrna.sgldfp
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbrna.sgldfp:  Program error
make[1]: [Makefile:1224: test.serial.pmemd.sgld] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb_rna && ./Run.gbrna.sgldg
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbrna.sgldg:  Program error
make[1]: [Makefile:1225: test.serial.pmemd.sgld] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gb_rna && ./Run.gbrna.sgmdg
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gbrna.sgmdg:  Program error
make[1]: [Makefile:1226: test.serial.pmemd.sgld] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd emap/ && ./Run.emap
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.emap:  Program error
make[1]: [Makefile:1544: test.serial.pmemd.emap] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd';  unset DO_PARALLEL; cd emil/emil_pmemd_gbsa && ./Run.emil EMIL
DO_PARALLEL not set... testing emil in serial.
  ./Run.emil:  Program error
make[1]: [Makefile:1504: test.serial.emil.pmemd] Error 1 (ignored)
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd';  unset DO_PARALLEL; cd emil/emil_pmemd_tip3p && ./Run.emil EMIL
DO_PARALLEL not set... testing emil in serial.
  ./Run.emil:  Program error
make[1]: [Makefile:1505: test.serial.emil.pmemd] Error 1 (ignored)
cd nfe && ./run-pmemd-serial.sh
>>>>>>> doing 'abmd_ANALYSIS'
>>>>>>> doing 'abmd_FLOODING'
>>>>>>> doing 'abmd_UMBRELLA'
>>>>>>> doing 'smd'
 ** Error ** : '/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2/bin/pmemd' is not executable
>>>>>>> doing 'smd2'
 ** Error ** : '/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2/bin/pmemd' is not executable
>>>>>>> doing 'pmd'
 ** Error ** : '/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2/bin/pmemd' is not executable
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd gamd && make -k test OPT=pmemd
make[2]: Entering directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/gamd'
Testing GaMD with PME
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pme.gamd1:  Program error
make[2]: [Makefile:7: pme] Error 1 (ignored)
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pme.gamd2:  Program error
make[2]: [Makefile:8: pme] Error 1 (ignored)
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pme.gamd3:  Program error
make[2]: [Makefile:9: pme] Error 1 (ignored)
Testing GaMD with GB
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gb.gamd1:  Program error
make[2]: [Makefile:13: gb] Error 1 (ignored)
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gb.gamd2:  Program error
make[2]: [Makefile:14: gb] Error 1 (ignored)
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gb.gamd3:  Program error
make[2]: [Makefile:15: gb] Error 1 (ignored)
make[2]: Leaving directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/gamd'
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd amd && make -k test OPT=pmemd
make[2]: Entering directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/amd'
Testing AMD with PME
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pme.amd1:  Program error
make[2]: [Makefile:7: pme] Error 1 (ignored)
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pme.amd2:  Program error
make[2]: [Makefile:8: pme] Error 1 (ignored)
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.pme.amd3:  Program error
make[2]: [Makefile:9: pme] Error 1 (ignored)
Testing AMD with GB
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gb.amd1:  Program error
make[2]: [Makefile:19: gb] Error 1 (ignored)
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gb.amd2:  Program error
make[2]: [Makefile:20: gb] Error 1 (ignored)
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.gb.amd3:  Program error
make[2]: [Makefile:21: gb] Error 1 (ignored)
make[2]: Leaving directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/amd'
export TESTsander='/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd'; cd scaledMD && make -k test OPT=pmemd
make[2]: Entering directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/scaledMD'
Testing scaledMD with PME
/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2///bin/pmemd: Command not found.
  ./Run.scaledMD:  Program error
make[2]: *** [Makefile:7: pme] Error 1
make[2]: Target 'test' not remade because of errors.
make[2]: Leaving directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test/scaledMD'
make[1]: [Makefile:1065: test.serial.pmemd.amd] Error 2 (ignored)
make[1]: Leaving directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test'
make[1]: Entering directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test'

Finished serial test suite for Amber 20 at Mon 18 Oct 09:24:50 BST 2021.

make[1]: Leaving directory '/dev/shm/build-branfosj-admin/branfosj-admin-up/AmberTools/20/intel-2020a-Python-3.8.2/test'
0 file comparisons passed
0 file comparisons failed
127 tests experienced errors
Test log file saved as /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/AmberTools/20-intel-2020a-Python-3.8.2/logs/test_amber_serial/2021-10-18_09-24-42.log
No test diffs to save!
make: *** [Makefile:15: test] Error 1

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And that is lots of pmemd not found failures.

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Ok, then that's something we should report upstreams... I'll ask David

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But somethings off here it should not go into test and run make test, it should go into AmberTools/test and run make test.
Was that the start of the test_step section?

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Even with the changes in easybuilders/easybuild-easyblocks#2604, I'm still running into test failures after removing the runtest = False here... :(

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@branfosj @akesandgren How about getting this merged, and figuring out the problems with the tests in the context of easybuilders/easybuild-easyblocks#2604?

This easyconfig is currently broken hard due to the changes in easybuilders/easybuild-easyblocks#2445, at least this way there's some progress...

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Just running a test report from my side....

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I'm happy to proceed here. I'm not sure I'll have time to look at easybuilders/easybuild-easyblocks#2604 soon, as it is clearly more complicated than I first thought.

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I've sent a question to the developers about AT testing, no reply yet though.


moduleclass = 'chem'
13 changes: 13 additions & 0 deletions easybuild/easyconfigs/a/AmberTools/AmberTools-20_cmake-locate-netcdf.patch
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@@ -0,0 +1,13 @@
Ensure that CMake recurses available paths if the Fortran libs aren't available in the netCDF module

James Carpenter 2021-01-23
--- amber20_src/cmake/jedbrown/FindNetCDF.cmake.orig 2020-04-28 02:19:51.000000000 +0100
+++ amber20_src/cmake/jedbrown/FindNetCDF.cmake 2021-01-25 11:41:47.005657000 +0000
@@ -52,6 +52,7 @@

macro (NetCDF_check_interface lang header libs)
find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}" NO_DEFAULT_PATH)
+ find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}")

find_library (NetCDF_LIBRARIES_${lang} NAMES ${libs} HINTS "${NetCDF_lib_dirs}")

21 changes: 21 additions & 0 deletions easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch
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@@ -0,0 +1,21 @@
When using "usempi" there will be no MPI_xxx_LIBRARIES set and that causes
import_libraries to error out. We know it is correct so comment out that
FATAL_ERROR.

Åke Sandgren, 2021-06-16
diff -ru AmberTools.orig/cmake/LibraryTracking.cmake AmberTools/cmake/LibraryTracking.cmake
--- AmberTools.orig/cmake/LibraryTracking.cmake 2021-04-25 02:51:44.000000000 +0200
+++ AmberTools/cmake/LibraryTracking.cmake 2021-06-16 13:30:26.568317368 +0200
@@ -170,9 +170,9 @@

cmake_parse_arguments(IMP_LIBS "" "" "LIBRARIES;INCLUDES" ${ARGN})

- if("${IMP_LIBS_LIBRARIES}" STREQUAL "")
- message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.")
- endif()
+ #if("${IMP_LIBS_LIBRARIES}" STREQUAL "")
+ # message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.")
+ #endif()

if(NOT "${IMP_LIBS_UNPARSED_ARGUMENTS}" STREQUAL "")
message(FATAL_ERROR "Incorrect usage. Extra arguments provided.")
19 changes: 19 additions & 0 deletions easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_xblas_missing_make_dependency.patch
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Fix a missing dependency in xblas causing problems when building with large -j

Åke Sandgren, 2021-07-01
diff -ru amber20_src.orig/AmberTools/src/xblas/Makefile amber20_src/AmberTools/src/xblas/Makefile
--- amber20_src.orig/AmberTools/src/xblas/Makefile 2020-01-02 18:26:09.000000000 +0100
+++ amber20_src/AmberTools/src/xblas/Makefile 2021-07-01 11:34:05.281580939 +0200
@@ -97,10 +97,10 @@
grep 'FAIL/TOTAL' testall.result >testall.summary
cat testall.summary

-common-lib:
+common-lib: header
cd $(SRC_DIR)/common && $(MAKE)

-common-test-lib:
+common-test-lib: header
cd $(TEST_DIR)/common && $(MAKE)