[gmx-users] Fwd: Trouble compiling gromacs 5.1.2 with plumed 2.2.3

[Anna Vernon]

---------- Forwarded message ----------
From: Anna Vernon <lappala.anna at gmail.com>
Date: 25 October 2016 at 10:55
Subject: Re: [gmx-users] Trouble compiling gromacs 5.1.2 with plumed 2.2.3
To: Giovanni Bussi <giovanni.bussi at gmail.com>
Cc: Carlo Camilloni <carlo.camilloni at gmail.com>


Giovanni,

My apologies, I have been doing this over a week and it is more than a
little frustrating at this stage.  From my first email you can see that yes
gromacs compiled and installed well on its own, and works. but after a
patch, it does not compile. As Mark said, it might be something MPI
related. To reiterate,

So... I compiled and installed  gmx 5.1.2 on its own and it was fine. I
patched it up with plumed 2.2.3 and it could not compile anymore.

The error message was this:

usr/bin/ld: ../../lib/libgromacs.so.1.2.0: undefined reference to symbol
'MPI_Isend'
//usr/lib/x86_64-linux-gnu/libmpich.so.12: error adding symbols: DSO
missing from command line
collect2: error: ld returned 1 exit status
share/template/CMakeFiles/template.dir/build.make:99: recipe for target
'bin/template' failed
make[2]: *** [bin/template] Error 1
CMakeFiles/Makefile2:1745: recipe for target
'share/template/CMakeFiles/template.dir/all'
failed
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

this is my gromacs cmake:

cmake .. -DGMX_MPI=on -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
-DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np -DNUMPROC=2, -DNUMPROC=3,
-DNUMPROC=4, -DNUMPROC=5, -DNUMPROC=6, -DNUMPROC=7,-DNUMPROC=8
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

after which i do make  and make, upon which the error message appears.

this is how I configure plumed:

./configure --enable-mpi CXX="$MPICXX" --prefix=/usr/local

What is going on?



On 25 October 2016 at 10:35, Giovanni Bussi <giovanni.bussi at gmail.com>
wrote:

> Hi,
>
> I don't think your chances to get a reply depends on you writing on
> private emails instead of using the official mailing list.
>
> From what you reported I did not even understand if you managed to compile
> and use gromacs as is (without plumed) so I honestly do not know how to
> help.
>
> Giovanni
>
> On Tue, Oct 25, 2016 at 6:33 PM, Anna Vernon <lappala.anna at gmail.com>
> wrote:
>
>>
>> ---------- Forwarded message ----------
>> From: Mark Abraham <mark.j.abraham at gmail.com>
>> Date: 25 October 2016 at 10:13
>> Subject: Re: [gmx-users] Trouble compiling gromacs 5.1.2 with plumed 2.2.3
>> To: gmx-users at gromacs.org, plumed-users at googlegroups.com
>>
>>
>> Hi,
>>
>> The simplest explanation would be that you're somehow actually using
>> different MPI compilers for the two stages. You should make sure you're
>> following the PLUMED installation instructions, and perhaps contact their
>> forums/whatever also. Your setup seems so vanilla that things should just
>> be working.
>>
>> Mark
>>
>> On Tue, Oct 25, 2016 at 4:39 PM Anna Vernon <lappala.anna at gmail.com>
>> wrote:
>>
>> > So... I compiled and installed  gmx 5.1.2 on its own and it was fine. I
>> > patched it up with plumed 2.2.3 and it could not compile anymore.
>> >
>> > The error message was this:
>> >
>> > usr/bin/ld: ../../lib/libgromacs.so.1.2.0: undefined reference to symbol
>> > 'MPI_Isend'
>> > //usr/lib/x86_64-linux-gnu/libmpich.so.12: error adding symbols: DSO
>> > missing from command line
>> > collect2: error: ld returned 1 exit status
>> > share/template/CMakeFiles/template.dir/build.make:99: recipe for target
>> > 'bin/template' failed
>> > make[2]: *** [bin/template] Error 1
>> > CMakeFiles/Makefile2:1745: recipe for target
>> > 'share/template/CMakeFiles/template.dir/all' failed
>> > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> > Makefile:160: recipe for target 'all' failed
>> > make: *** [all] Error 2
>> >
>> > this is my gromacs cmake:
>> >
>> > cmake .. -DGMX_MPI=on -DCMAKE_C_COMPILER=mpicc
>> -DCMAKE_CXX_COMPILER=mpicxx
>> > -DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np -DNUMPROC=2, -DNUMPROC=3,
>> > -DNUMPROC=4, -DNUMPROC=5, -DNUMPROC=6, -DNUMPROC=7,-DNUMPROC=8
>> > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>> >
>> > after which i do make  and make, upon which the error message appears.
>> >
>> > this is how I configure plumed:
>> >
>> > ./configure --enable-mpi CXX="$MPICXX" --prefix=/usr/local
>> >
>> > What is going on?
>> >
>> > Anna
>> > --
>> > Gromacs Users mailing list
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>