Dear developers and users,
I tried to install AMBER from source on my laptop and work desktop. Both times I followed the 2023 Reference Manual and had partially similar problems with the Perl module Chemistry. I've included for you the details of my systems and the corresponding cmake error output. Thanks in advance.
Both installations were performed with the same cmake keys below.
run_cmake content:
cmake $AMBER_PREFIX/amber22_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 \
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
1. Work desktop.
OS and compiler's version:
OS: Ubuntu 22.04.3 LTS
gcc (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 10.3.0-15ubuntu1) 10.3.0
cmake version 3.22.1
nvcc: Cuda compilation tools, release 11.5, V11.5.119
CMakeError.log:
Performing C SOURCE FILE Test CMath_LINKS_WITHOUT_M failed with the following output:
Change Dir: /scratch/ildar/software/amber22_src/build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_9bc1e/fast && /usr/bin/gmake -f CMakeFiles/cmTC_9bc1e.dir/build.make CMakeFiles/cmTC_9bc1e.dir/build
gmake[1]: Entering directory '/scratch/ildar/software/amber22_src/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_9bc1e.dir/src.c.o
/usr/bin/gcc -DCMath_LINKS_WITHOUT_M -fPIE -std=gnu99 -o CMakeFiles/cmTC_9bc1e.dir/src.c.o -c /scratch/ildar/software/amber22_src/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_9bc1e
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_9bc1e.dir/link.txt --verbose=1
/usr/bin/gcc CMakeFiles/cmTC_9bc1e.dir/src.c.o -o cmTC_9bc1e
/usr/bin/ld: CMakeFiles/cmTC_9bc1e.dir/src.c.o: in function `main':
src.c:(.text+0x2c): undefined reference to `sin'
collect2: error: ld returned 1 exit status
gmake[1]: *** [CMakeFiles/cmTC_9bc1e.dir/build.make:99: cmTC_9bc1e] Error 1
gmake[1]: Leaving directory '/scratch/ildar/software/amber22_src/build/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:127: cmTC_9bc1e/fast] Error 2
Source file was:
#include <math.h>
int main(int argc, char** argv)
{
return sin(argc - 1);
}
Determining if the Perl module Chemistry::Mol exists failed with the following error output:
Can't locate Chemistry/Mol.pm in @INC (you may need to install the Chemistry::Mol module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
1. Personal laptop
OS and compiler's version:
OS: Kubuntu 22.04.3 LTS
gcc (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
cmake version 3.22.1
nvcc: Cuda compilation tools, release 11.5, V11.5.119
CMakeError.log:
Determining if the Perl module Chemistry::Mol exists failed with the following error output:
Can't locate Chemistry/Mol.pm in .INC (you may need to install the Chemistry::Mol module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
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Received on Tue Jan 30 2024 - 01:30:02 PST
