Re: [AMBER] Amber18 compilation error on a Linux CPU cluster

From: Sundar <>
Date: Mon, 24 Dec 2018 19:16:49 -0600


I followed your instructions and ran following commands.
cd $AMBERHOME/AmberTools/src
./configure_mpich gnu

And successfully compiled mpich-3.3 within the folder after downloading it
After that do I need to compile the parallel version using
./configure -mpi gnu" and rest of the commands as listed in Amber User

If yes,
"./configure -mpi gnu" gives me following errors.

sundar.copper01:~/tools/amber18/amber18> ./configure -mpi gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...

Available AmberTools 18 patches:

No patches available

Available Amber 18 patches:

No patches available


Using the AmberTools miniconda installation in
version 2.7.13

Obtaining the gnu compiler suite versions, e.g.:
     gcc -v
The C version is 4.3.4
The Fortran version is 4.3.4

Testing the gcc compiler:
     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c

Testing the CC compiler:
     CC -fPIC -o testp testp.cpp

Testing the gfortran compiler:
     gfortran -fPIC -O0 -o testp testp.f

Testing mixed C/Fortran compilation:
     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
     gfortran -fPIC -O0 -c -o testp.f.o testp.f
testp.c.o testp.f.o -lgfortran -w
/usr/lib64/gcc/x86_64-suse-linux/4.3/libgfortran.a(fpu.o): In function
undefined reference to `fedisableexcept'
undefined reference to `feenableexcept'
undefined reference to `feenableexcept'
undefined reference to `feenableexcept'
undefined reference to `feenableexcept'
undefined reference to `feenableexcept'
collect2: ld returned 1 exit status
./configure2: line 2643: ./testp: No such file or directory
Error: Unable to compile mixed C/Fortran code.
       Please check your compiler settings and configure flags.
Configure failed due to the errors above!


On Mon, Dec 24, 2018 at 9:32 AM David Case <> wrote:

> On Sun, Dec 23, 2018, Sundar wrote:
> >$ tail $AMBERHOME/AmberTools/src/fftw3_config.log
> >
> >checking for mpicc... no
> >checking for hcc... no
> >checking for mpcc... no
> >checking for mpcc_r... no
> >checking for mpxlc... no
> >checking for cmpicc... no
> >checking for MPI_Init... no
> >checking for MPI_Init in -lmpi... no
> >checking for MPI_Init in -lmpich... no
> >configure: error: could not find mpi library for --enable-mpi
> It looks like your mpi installation is not correct, and this is the
> first part of the installation script that catches this.
> What MPI are you using? What is the result of typing "which mpicc"?
> (This executable, along with mpif90, needs to be in your PATH).
> The most straighforward method is to cd $AMBERHOME/AmberTools/src, and
> run either configure_mpich or configure_openmpi there. This sets up the
> correct executables and libraries, all inside the AMBERHOME folder.
> You can also install MPI via package managers; details vary depending on
> which version of Linux or MacOS you have. But make sure that those
> installations are using the same compilers as you use for compiling the
> rest of Amber.
> ...good luck...dac

Sundar Thangapandian
AMBER mailing list
Received on Mon Dec 24 2018 - 17:30:02 PST
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