Re: [AMBER] mpi installation problem

From: Prabir Khatua <>
Date: Mon, 4 Feb 2019 22:51:32 +0530

By mistake, I gave the wrong information about serial version in this
server where I got the similar problem too. Once again, I could not
understand the problem by looking
at the mentioned log file. Following is the error.
Checking NetCDF...
    Using bundled NetCDF library.
    Starting NetCDF build.
    Configuring NetCDF C interface (may be time-consuming)...
Error: NetCDF C configure returned 1
       NetCDF configure failed! Check the netcdf_config.log file
       in the /home/prabir/SOFTWARE/AMBER/amber14/AmberTools/src directory.
Configure failed due to the errors above!
[prabir.c474 amber14]$ vi

Attached is the corresponding log file.

On Mon, Feb 4, 2019 at 10:36 PM Prabir Khatua <>

> Dear Sir,
> Thank you very much for your reply. It is to be noted that the server
> where I am trying to install amber has openmpi enabled mpi.
> mpicc is located in
> /opt/oscer/software/openmpi/1.10.3/intel/avx-shm-mxm/bin. I am loading this
> module before configuring amber
> with mpi. I am trying to install amber in the following $AMBERHOME
> directory
> /home/prabir/SOFTWARE/AMBER/AMBER14/amber14
> mpicc is in the $PATH as per my understanding. However, I am not sure
> whether compiler used for serial version is same as that
> of mpi version. Can you please tell me the command to check it. I tried to
> check it by typing "mpicc -show". However, it showed that
> this commad does not exist. I am sharing the log file. I really did not
> understand the error from this log file. Please advice me to fix
> this problem.
> Thank you,
> Sincerely,
> Prabir
> On Sat, Feb 2, 2019 at 10:38 PM David Case <> wrote:
>> On Fri, Feb 01, 2019, Prabir Khatua wrote:
>> >
>> >I am experiencing a problem in installing Amber 14 with Amber15Tools with
>> >mpi. Following is the error that I am getting while I was trying to
>> >configure it with mpi
>> >
>> >Error: FFTW configure returned 1
>> > FFTW configure failed! Check the fftw3_config.log file
>> > in the /home/prabir/SOFTWARE/AMBER/AMBER14/amber14/AmberTools/src
>> >directory.
>> So: what was the result of looking at the log file described above?
>> That will tell you what the problem is. Be sure that files like mpicc
>> are in your $PATH, and that the compilers used match those you used of
>> the serial installation--type "mpicc -show" to find this out.
>> But this is all guesswork: look at the log file and see if that helps.
>> If you still have problems, please let us know what is in that file.
>> ...good luck....dac
>> p.s. Amber14 is five years old, which is a long time in software terms.
>> Consider upgrading to AmberTools18.
>> _______________________________________________
>> AMBER mailing list
> --
> *Prabir Khatua*
> *Postdoctoral Research Associate*
> *Department of Chemistry & Biochemistry*
> *University of Oklahoma*
> *Norman, Oklahoma 73019*
> *U. S. A.*

*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*

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Received on Mon Feb 04 2019 - 09:30:02 PST
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