[gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0

[Szilárd Páll]

On Sat, Apr 4, 2020 at 10:41 PM Wei-Tse Hsu <Weitse.Hsu at colorado.edu> wrote:

> Dear gmx users,
> Recently I've been trying to install GROMACS 2020.1. However, I encounter a
> compilation error while using the make command. The error is as follows:
>
>
>
>
>
> */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find
> /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit
> statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2*
> From the error above, it seemed that GROMACS was unable to find library
> like libpthread.so.0 and libpthread_nonshared.a. After checking I found
> that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and
> libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/
> x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add
> the paths of the libraries for GROMACS to search for. Specifically, the
> command I was using is:
> *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd
> build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON
> -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7
> -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make
>

As Kevin noted, the separator in the prefix path should be ";".

However, it seem unnecessary to pass system libraries as custom paths to
cmake. Try first without those.

--
Szilárd



> > gmx_compile.log*
> However, it turned out that I still got the same error. I'm confused right
> now since I thought that gromacs should be able to find the files. I'm
> wondering if I missed something. Could someone please tell me what I can do
> or share some relevant experience? Any help is much appreciated!
>
> Best,
> Wei-Tse
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