Hi David,
Thanks, David. I set AMBERHOME variable (/data/Amber/amber20) and run amber.sh from /data/Amber/amber20
Lines in amber.sh
if [ -n "$BASH_SOURCE" ]; then
this_script="$BASH_SOURCE"
elif [ -n "$DASH_SOURCE" ]; then
this_script="$DASH_SOURCE"
elif [ -n "$ZSH_VERSION" ]; then
setopt function_argzero
this_script="$0"
elif eval '[[ -n ${.sh.file} ]]' 2>/dev/null; then
eval 'this_script=${.sh.file}'
else
echo 1>&2 "Unsupported shell. Please use bash, dash, ksh93 or zsh."
exit 2
fi
export AMBERHOME=$(cd "$(dirname "$this_script")"; pwd)
export PATH="$AMBERHOME/bin:$PATH"
# Add Amber lib folder to LD_LIBRARY_PATH (if your platform supports it)
# Note that LD_LIBRARY_PATH is only necessary to help Amber's Python programs find their dynamic libraries,
# unless Amber has been moved from where it was installed.
if [ 1 = 1 ]; then
if [ -z "$LD_LIBRARY_PATH" ]; then
export LD_LIBRARY_PATH="$AMBERHOME/lib"
else
export LD_LIBRARY_PATH="$AMBERHOME/lib:$LD_LIBRARY_PATH"
fi
fi
# Add location of Amber Perl modules to default Perl search path (if your platform supports it)
if [ 1 = 1 ]; then
if [ -z "$PERL5LIB" ]; then
export PERL5LIB="$AMBERHOME/lib/perl"
else
export PERL5LIB="$AMBERHOME/lib/perl:$PERL5LIB"
fi
fi
Then I ran – make test.serial. Below are the last few lines from error message:
./Run.pme.amd2: Program error
make[3]: [pme] Error 1 (ignored)
gbin: Permission denied.
Unit 5 Error on OPEN: gbin
Unit 5 Error on OPEN: gbin
STOP PMEMD Terminated Abnormally!
./Run.pme.amd3: Program error
make[3]: [pme] Error 1 (ignored)
Testing AMD with GB
gbin: Permission denied.
Unit 5 Error on OPEN: gbin
Unit 5 Error on OPEN: gbin
STOP PMEMD Terminated Abnormally!
./Run.gb.amd1: Program error
make[3]: [gb] Error 1 (ignored)
gbin: Permission denied.
Unit 5 Error on OPEN: gbin
Unit 5 Error on OPEN: gbin
STOP PMEMD Terminated Abnormally!
./Run.gb.amd2: Program error
make[3]: [gb] Error 1 (ignored)
gbin: Permission denied.
Unit 5 Error on OPEN: gbin
Unit 5 Error on OPEN: gbin
STOP PMEMD Terminated Abnormally!
./Run.gb.amd3: Program error
make[3]: [gb] Error 1 (ignored)
make[3]: Leaving directory `/data/Amber/amber20/test/amd'
export TESTsander='/data/Amber/amber20///bin/pmemd'; cd scaledMD && make -k test OPT=pmemd
make[3]: Entering directory `/data/Amber/amber20/test/scaledMD'
Testing scaledMD with PME
mdin: Permission denied.
Unit 5 Error on OPEN: mdin
Unit 5 Error on OPEN: mdin
STOP PMEMD Terminated Abnormally!
./Run.scaledMD: Program error
make[3]: *** [pme] Error 1
make[3]: Target `test' not remade because of errors.
make[3]: Leaving directory `/data/Amber/amber20/test/scaledMD'
make[2]: [test.serial.pmemd.amd] Error 2 (ignored)
make[2]: Leaving directory `/data/Amber/amber20/test'
tee: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
make[2]: Entering directory `/data/Amber/amber20/test'
Finished serial test suite for Amber 20 at Wed Dec 22 10:25:43 EST 2021.
make[2]: Leaving directory `/data/Amber/amber20/test'
grep: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
grep: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
grep: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
grep: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
tee: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
0 file comparisons passed
tee: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
0 file comparisons failed
tee: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
0 tests experienced errors
tee: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
Test log file saved as /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log
tee: /data/Amber/amber20/logs/test_amber_serial/2021-12-22_10-25-41.log: No such file or directory
No test diffs to save!
make[1]: Leaving directory `/data/Amber/amber20/test'
Summary of AmberTools serial tests:
cat: ../logs/test_at_serial/at_summary: No such file or directory
make: *** [test.serial] Error 1
Regards
Suguna
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, December 21, 2021 11:32 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber20 installation error on Centos 7
Email from external sender: david.case.rutgers.edu<mailto:david.case.rutgers.edu>
On Tue, Dec 21, 2021, Suguna Sakkiah wrote:
>[ssakkiah.schrogpu1 amber20]$ make test.serial
>(cd AmberTools/test && make test)
>make[1]: Entering directory `/data/Amber/amber20/AmberTools/test'
>Makefile:2: /config.h: No such file or directory
Looks like you didn't set your AMBERHOME variable, by running the "amber.sh"
script in /data/Amber/amber20. Make sure that 'echo $AMBERHOME' gives
back this directory.
....dac
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Received on Wed Dec 22 2021 - 08:00:03 PST
