[Nek5000-users] Undefined references when compiling

[nek5000-users at lists.mcs.anl.gov]

Hi JP,


Perhaps makenek clean first ?


Paul


________________________________
From: Nek5000-users <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
Sent: Wednesday, November 15, 2017 6:39:51 PM
To: nek5000-users at lists.mcs.anl.gov
Subject: [Nek5000-users] Undefined references when compiling

Hi all,

I've never had any problem when compiling (in my personal computer or in the cluster server where I run simulations). Now I'm trying to use the latest version of Nek, and it worked in my computer but when I try to compile a case in the cluster I get errors.

Attached is the full compiler.out file, but the final part is:


[...]
/user/r/robinson/Nek5000/3rd_party/gslib/src/libgs.a(amg.o): In function `dread_mpi.isra.22':
amg.c:(.text+0x53b): undefined reference to `ompi_mpi_double'
/user/r/robinson/Nek5000/3rd_party/gslib/src/libgs.a(amg.o): In function `dopen_mpi.constprop.27':
amg.c:(.text+0x5eb): undefined reference to `ompi_mpi_info_null'
/user/r/robinson/Nek5000/3rd_party/gslib/src/libgs.a(amg.o): In function `gslib_crs_amg_setup':
amg.c:(.text+0x18d2): undefined reference to `ompi_mpi_unsigned_char'
amg.c:(.text+0x1cc1): undefined reference to `ompi_mpi_unsigned_char'
amg.c:(.text+0x1cde): undefined reference to `ompi_mpi_unsigned_char'
amg.c:(.text+0x1cfb): undefined reference to `ompi_mpi_unsigned_char'
amg.c:(.text+0x1dcb): undefined reference to `ompi_mpi_unsigned_char'
/user/r/robinson/Nek5000/3rd_party/gslib/src/libgs.a(amg.o):amg.c:(.text+0x1df1): more undefined references to `ompi_mpi_unsigned_char' follow
collect2: ld returned 1 exit status
make: *** [nek5000] Error 1


I notice that there are a lot of undefined references related to MPI. One differences is that in my computer I have openmpi but the cluster has mpich. Perhaps it is related with that, although when I use previous versions of Nek I have no problem in the cluster.

I can notice too that all the errors come from  Nek5000/3rd_party/gslib/src.
I went into that folder and realized that maybe I should install gslib libraries, and that means asking for the cluster administrator to do it.

What do you think I should do?

Thanks in advance,

JP.



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