Hi David,
Thanks for your suggestions. Changed the directory to /data/amber20/test and run the make test.serial from the Root login.
Now it shows the below error.
cd sanderapi && make test
make[1]: Entering directory `/data/Amber/amber20/test/sanderapi'
(if [ -f "/opt/miniconda3///lib/libsander.so" ]; then \
make test_all; \
else \
make test_none; \
fi;)
make[2]: Entering directory `/data/Amber/amber20/test/sanderapi'
Testing the Fortran API
/opt/miniconda3/bin/x86_64-conda-linux-gnu-gfortran -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniconda3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/ambertools_1626970347023/work=/usr/local/src/conda/ambertools-21.4 -fdebug-prefix-map=/opt/miniconda3=/usr/local/src/conda-prefix -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -I/opt/miniconda3///include -L/opt/miniconda3///lib test.F90 -o testf -lsander
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3///lib/././././libcrypto.so.1.1: undefined reference to `__fdelt_chk.GLIBC_2.15'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3///lib/./libstdc++.so.6: undefined reference to `aligned_alloc.GLIBC_2.16'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3///lib/././././libcrypto.so.1.1: undefined reference to `memcpy.GLIBC_2.14'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3///lib/./libstdc++.so.6: undefined reference to `clock_gettime.GLIBC_2.17'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3///lib/././././libcrypto.so.1.1: undefined reference to `getauxval.GLIBC_2.16'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3///lib/././././libcrypto.so.1.1: undefined reference to `secure_getenv.GLIBC_2.17'
collect2: error: ld returned 1 exit status
Program error
make[2]: *** [testf] Error 1
make[2]: Leaving directory `/data/Amber/amber20/test/sanderapi'
make[1]: *** [test] Error 2
make[1]: Leaving directory `/data/Amber/amber20/test/sanderapi'
make: [test.serial.sanderapi] Error 2 (ignored)
cd sanderlesapi && make test
make[1]: Entering directory `/data/Amber/amber20/test/sanderlesapi'
(if [ -f "/opt/miniconda3///lib/libsanderles.so" ]; then \
make test_all; \
else \
make test_none; \
fi;)
make[2]: Entering directory `/data/Amber/amber20/test/sanderlesapi'
Testing the Fortran LES API
/opt/miniconda3/bin/x86_64-conda-linux-gnu-gfortran -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniconda3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/ambertools_1626970347023/work=/usr/local/src/conda/ambertools-21.4 -fdebug-prefix-map=/opt/miniconda3=/usr/local/src/conda-prefix -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -I/opt/miniconda3/include -L/opt/miniconda3/lib test.F90 -o testf -lsanderles
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3/lib/././././libcrypto.so.1.1: undefined reference to `__fdelt_chk.GLIBC_2.15'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3/lib/./libstdc++.so.6: undefined reference to `aligned_alloc.GLIBC_2.16'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3/lib/././././libcrypto.so.1.1: undefined reference to `memcpy.GLIBC_2.14'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3/lib/./libstdc++.so.6: undefined reference to `clock_gettime.GLIBC_2.17'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3/lib/././././libcrypto.so.1.1: undefined reference to `getauxval.GLIBC_2.16'
/opt/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/miniconda3/lib/././././libcrypto.so.1.1: undefined reference to `secure_getenv.GLIBC_2.17'
collect2: error: ld returned 1 exit status
Program error
make[2]: *** [testf] Error 1
make[2]: Leaving directory `/data/Amber/amber20/test/sanderlesapi'
make[1]: *** [test] Error 2
make[1]: Leaving directory `/data/Amber/amber20/test/sanderlesapi'
make: [test.serial.sanderapi] Error 2 (ignored)
Regards
Suguna
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, December 22, 2021 8:56 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 Wed, Dec 22, 2021, Suguna Sakkiah wrote:
>
>Thanks, David. I set AMBERHOME variable (/data/Amber/amber20) and run amber.sh from /data/Amber/amber20
Just be sure that 'echo $AMBERHOME' yields the expected result.
>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.
Did every test fail? Or almost every test? I've not seen this before, but
it might be that you don't have write permissions in your $AMBERHOME
hierarchy(?) Try this:
cd $AMBERHOME/AmberTools/test
echo 'abc' > def
Do you get any error message?
....dac
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Received on Thu Dec 23 2021 - 11:30:03 PST
