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

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akesandgren merged 7 commits intoeasybuilders:developfrom
boegel:20210917202853_new_pr_AmberTools20
Oct 21, 2021
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fix AmberTools v20 easyconfig using intel/2020a toolchain#14028
akesandgren merged 7 commits intoeasybuilders:developfrom
boegel:20210917202853_new_pr_AmberTools20

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@boegel boegel commented Sep 17, 2021

(created using eb --new-pr)
fixes #14021

@boegel boegel marked this pull request as draft September 17, 2021 18:29
@boegel boegel added this to the next release (4.5.0?) milestone Sep 17, 2021
@boegel boegel added the bug fix label Sep 17, 2021
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akesandgren
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Comment thread easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb Outdated
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Comment thread easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb Outdated
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branfosj commented Sep 25, 2021

I see the following failure:

gcc: error: source: No such file or directory
gcc: error: unrecognized command line option -ftz
gcc: error: unrecognized command line option -fp-speculation=safe
gcc: error: unrecognized command line option -fp-model; did you mean -ftls-model=?
error: command 'gcc' failed with exit status 1

Setting configopts = '-DBUILD_SANDER_API=OFF' bypasses that error. I expect this is why configopts = "-nosanderapi" was included. However, the issue in the above error is that Cython is using gcc in the linking stage. Adding

prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' %(builddir)s/AmberTools/src/pysander/setup.py && """

fixes this issue.

I also had to disable the tests (with runtest = False) as they try to run pmemd and that is not part of AmberTools (CMake log says pmemd - Not included in AmberTools).

And the Amber-20_fix-hardcoding.patch is not needed - as it edits configure2 and this is not used in a CMake build.

With those changes I can successfully build AmberTools 20.

@branfosj branfosj mentioned this pull request Oct 14, 2021
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branfosj commented Oct 14, 2021

@boegel my suggested fix is in boegel#83

@boegel boegel changed the title fix AmberTools v20 easyconfig (WIP) fix AmberTools v20 easyconfig using intel/2020a toolchain Oct 14, 2021
@easybuilders easybuilders deleted a comment from boegelbot Oct 14, 2021
@boegel boegel marked this pull request as ready for review October 14, 2021 20:42
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boegel commented Oct 14, 2021

@boegelbot please test @ generoso
CORE_CNT=16

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boegel commented Oct 14, 2021

Should be good to go now, test reports coming up. Thanks for the help here @branfosj!

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boegelbot commented Oct 14, 2021

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=14028 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14028 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 7090

Test results coming soon (I hope)...

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it is of no use to you (unless you think I have a bug, which I don't).

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boegelbot commented Oct 14, 2021

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cnx1 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/d66851eeaa41a60e3c753c61bd6313b0 for a full test report.

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boegel commented Oct 14, 2021

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3139.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/efadc9c951115fbf7762967ed894a328 for a full test report.

akesandgren
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Comment thread easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb
@branfosj branfosj mentioned this pull request Oct 16, 2021
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Merge pull request #84 from branfosj/at_review
d0842d5 
add xblas patch and flex & make deps
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boegel commented Oct 16, 2021

@boegelbot please test @ generoso
CORE_CNT=16

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boegelbot commented Oct 16, 2021

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=14028 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14028 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 7096

Test results coming soon (I hope)...

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- notification for comment with ID 944886873 processed

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branfosj commented Oct 16, 2021

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/dd54a9333699d44d6d00ddbc0dde7bec for a full test report.

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cnx1 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/6e83a2a14cec3ccbdf18b8591f6cfa78 for a full test report.

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boegel commented Oct 16, 2021

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node2625.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/bf43e3848e654466d0219b005cd07636 for a full test report.

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boegel commented Oct 16, 2021

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3170.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/f4f8d49a9473e4d3ba063f547d513470 for a full test report.

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boegel commented Oct 16, 2021

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3553.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/533b5f8ddb29160cb181f27875fa9a13 for a full test report.

@boegel boegel requested a review from akesandgren October 16, 2021 15:00
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Comment thread easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb
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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@branfosj branfosj Oct 18, 2021

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And that is lots of pmemd not found failures.

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@akesandgren akesandgren Oct 18, 2021

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

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@akesandgren akesandgren Oct 18, 2021

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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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@boegel boegel Oct 20, 2021

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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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@boegel boegel Oct 20, 2021

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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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@akesandgren akesandgren Oct 21, 2021

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

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@branfosj branfosj Oct 21, 2021

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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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@akesandgren akesandgren Oct 21, 2021

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

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akesandgren commented Oct 21, 2021

Test report by @akesandgren
SUCCESS
Build succeeded for 4 out of 4 (1 easyconfigs in total)
b-an02.hpc2n.umu.se - Linux Ubuntu 20.04, x86_64, Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, Python 3.8.10
See https://gist.github.com/a382e630518226ce18d202ebe0dfccd3 for a full test report.

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akesandgren commented Oct 21, 2021

Going in, thanks @boegel!

@akesandgren akesandgren merged commit e182c0f into easybuilders:develop Oct 21, 2021
@boegel boegel deleted the 20210917202853_new_pr_AmberTools20 branch October 21, 2021 09:06
@branfosj branfosj mentioned this pull request Nov 30, 2021
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4.5.0

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installation of AmberTools v20 is broken due to switch to CMake in custom easyblock for Amber

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@boegel @branfosj @boegelbot @akesandgren