Re: [AMBER-Developers] [AMBER] Fwd: Fwd: Re: Is it a bug? Compilation Error in Ambertools

From: Jason Swails <>
Date: Tue, 25 Jun 2013 11:08:38 -0400

On Tue, Jun 25, 2013 at 10:44 AM, David A Case <>wrote:

> On Tue, Jun 25, 2013, Matthias Bohner wrote:
> >
> > $CC is gcc
> > $CXX is empty
> > $F90 is empty
> > $F77 is g95
> > $FC is g95
> >
> > unset CC CXX F90 F77 FC
> >
> > also solved the problem in my case.
> I'm guessing that the "g95" was the problem: netcdf was trying to use g95
> rather than gfortran. We should probably force the correct variables
> in the netcdf configure step.

I think we already do this (unless I'm missing something).
(configure2:1917) FWIW, on the machine where I had problems this was my

[swails . UF HPC ~] $ echo $CC $CXX $F90 $F77 $FC
mpicc mpicxx mpif90 mpif77
[swails . UF HPC ~] $ mpicc -show
icc -I/usr/mpi/intel/openmpi-1.6/include -pthread -L/usr/lib64 -Wl,-rpath
-Wl,/usr/mpi/intel/openmpi-1.6/lib64 -L/usr/mpi/intel/openmpi-1.6/lib64
-lmpi -lrdmacm -libverbs -lrt -lnsl -lutil -ltorque -ldl -lm
-Wl,--export-dynamic -lrt -lnsl -lutil
[swails . UF HPC ~] $ mpif90 -show
ifort -I/usr/mpi/intel/openmpi-1.6/include
-I/usr/mpi/intel/openmpi-1.6/lib64 -L/usr/lib64 -Wl,-rpath
-Wl,/usr/mpi/intel/openmpi-1.6/lib64 -L/usr/mpi/intel/openmpi-1.6/lib64
-lmpi_f90 -lmpi_f77 -lmpi -lrdmacm -libverbs -lrt -lnsl -lutil -ltorque
-ldl -lm -Wl,--export-dynamic -lrt -lnsl -lutil
[swails . UF HPC ~] $ mpicxx -show
icpc -I/usr/mpi/intel/openmpi-1.6/include -pthread -L/usr/lib64 -Wl,-rpath
-Wl,/usr/mpi/intel/openmpi-1.6/lib64 -L/usr/mpi/intel/openmpi-1.6/lib64
-lmpi_cxx -lmpi -lrdmacm -libverbs -lrt -lnsl -lutil -ltorque -ldl -lm
-Wl,--export-dynamic -lrt -lnsl -lutil
[swails . UF HPC ~] $ mpif77 -show
ifort -I/usr/mpi/intel/openmpi-1.6/include -L/usr/lib64 -Wl,-rpath
-Wl,/usr/mpi/intel/openmpi-1.6/lib64 -L/usr/mpi/intel/openmpi-1.6/lib64
-lmpi_f77 -lmpi -lrdmacm -libverbs -lrt -lnsl -lutil -ltorque -ldl -lm
-Wl,--export-dynamic -lrt -lnsl -lutil

And I specified the Intel compilers, so those compilers should have been
fine. I'm still not sure why I got the reported error or why unsetting
those variables fixed my problem... This was the local UF HPC, not a
change I would've made to my own environment.

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Jun 25 2013 - 08:30:03 PDT
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