Ildar,
(1) sudo apt install libchemistry-mol-perl
(2) Try this as your run_cmake, note you will have to make install with
sudo otherwise change -DCMAKE_INSTALL_PREFIX but be sure to keep the
additional 2 flags I have here:
cmake $AMBER_PREFIX/amber22_src \
-DCMAKE_INSTALL_PREFIX=/usr/local/amber22 \
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=FALSE -DAPPLY_UPDATES=TRUE \
-DTRUST_SYSTEM_LIBS=TRUE \
2>&1 | tee cmake.log
(3) Report back.
Cheers,
Todd
On Tue, Jan 30, 2024 at 3:10 AM Ildar Garipov via AMBER <amber.ambermd.org>
wrote:
> 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 - 07:30:02 PST
