Hi David,
I installed the gfortran and rerun the test.serial. I am not planning to run sander, so can I ignore all the below error message and move to the next step of installation by changing the CUDA=TRUE in the run_camke file?
diffing emil.log.0.9.save with emil.log.0.9
PASSED
==============================================================
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_artifact s/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<mailto:_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_g ettime.GLIBC_2.17<mailto:ettime.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_artifact s/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<mailto:_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<mailto:lloc.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 `m emcpy.GLIBC_2.14<mailto:emcpy.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_get time.GLIBC_2.17<mailto:time.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<mailto:etauxval.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<mailto:ecure_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: Friday, December 24, 2021 9:16 AM
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 Thu, Dec 23, 2021, Suguna Sakkiah wrote:
>
>Thanks for your suggestions. Changed the directory to /data/amber20/test
>and run the make test.serial from the Root login.
>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'
First: are you ever planning to use the Fortran API to sander? (This is
exceedingly rare). If not, you can ignore these errors.
Second, what is the result of typing "which gfortran" and "gfortran
--version"? It looks like you are using a miniconda version that was not
installed by Amber (since that would be located at
/data/Amber/amber20/miniconda).
To get started better, find a file location in which you have write
privileges; do an initial install using the default run_cmake script. After
that, one can start adding features.
....good luck...dac
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Received on Fri Dec 24 2021 - 16:00:02 PST
