Thanks Dave and Daniel for your answers to this,
I am trying to clarify this with the support at the supercomputer center
... Indeed when I test with "mpicc -show" and "mpicc -v" it appears as
the Intel MPI is compiled with gcc 4.8.5 ... So, maybe here is the
incompatibility ... But this was not a problem with gcc 7.4 with which
I could compile also using an MPI built with gcc 4.8.5 ....
Unfortunately using another MPI than the Intel MPI they provide its not
that straight forward but will look into that as well ...
Best
Vlad
/> /
/>I am trying to compile Amber 18 with AmberTools 19 on a supercomputer. /
/>I tried using the default environment that provides intel mpi 2019 and /
/>gcc 9.2.0 ... However, when trying to compile the MPI executables I /
/>get the error attached here ... /
[SANDER] FC remd.F90
f951: Fatal Error: Reading module ‘mpi’ at line 1 column 2: Unexpected EOF
compilation terminated.
Vlad: the mpi module that remd.F90 is looking for in its "use mpi" statment
does not come from Amber, but rather from your mpi installation. Are
you sure your MPI stack was compiled with gcc9.2? A quick look at the
output of 'mpicc -show' might help.
My suggestion (as usual): use the configure_mpich script in
AMBERHOME/AmberToosl/src to build your own MPI, making sure it is using
the same compilers you are using to build the rest of Amber.
Of course, the problem could be elsewhere, but your error message looks
like an incomptibility between the compiler and the module file for mpi.
....dac
On 10/28/19 3:57 PM, Vlad Cojocaru wrote:
> Dear all,
>
> I am trying to compile Amber 18 with AmberTools 19 on a supercomputer.
> I tried using the default environment that provides intel mpi 2019 and
> gcc 9.2.0 ... However, when trying to compile the MPI executables I
> get the error attached here ...
>
> Previously I was able to compile on the same machine with impi 2018
> and gcc 7.4 .. Now gcc 7 is not available anymore
>
> I am not able to fully understand this "unexpected end of file issue"
> but I thought it looks more like a coding issue than an environment
> issue. So I thought asking here is more appropriate than at the
> computing center ....
>
> Has anyone seen anything similar and if yes, any idea how to fix it ?
>
> Thank you for any advise
>
> Best wishes
> Vlad
>
>
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Thu Nov 07 2019 - 07:00:02 PST
