Re: [AMBER] AMBER16 parallelisation and fftw3 error

From: Shirin Jamshidi <>
Date: Fri, 6 Oct 2017 22:45:02 +0100

Thanks David and Hai!

I have completed the problem with pmemd.cuda.MPI command:

After serial and parallel installation of AMBER, I have installed
as below

./configure -cuda -mpi gnu
make install
export DO_PARALLEL="mpirun -np 2"
make test
cd $AMBERHOME/AmberTools/src
./configure_mpich gnu

Then for getting rid of the below error to be able to run cuda command on
GPU nodes,
​Error: ​ cannot open shared object file: No such file or directory

I double checked that I have exported the LD_LIBRARY_PATH with either of
the below commands:

export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64


sudo ldconfig /usr/local/cuda/lib64

But I have to do it every time that I restarted.

It seems every thing is sorted now, but my only concern is that I had some
error in make test section. Just was wondering if I should ignore them or
solve that issue as well.

Also I was wondering how I can put the exporting of the LD_LIBRARY_PATH in
the path.

Thanks for any advice in advance.



On Fri, Oct 6, 2017 at 2:37 PM, Shirin Jamshidi <>

> Thanks for your reply and your correction.
> Actually I ado need pmemd.cuda.MPI command to run production step of MD
> simulation with amber on the GPU nodes of my workstation.
> I repeat the parallel installation as below:
> ./configure -mpi gnu
> make install
> make test
> cd $AMBERHOME/AmberTools/src
> ./configure_mpich gnu
> now sander.MPI is built.
> How can I able to have pmemd.cuda.MPI as well?
> Best,
> Shirin
> On Fri, Oct 6, 2017 at 1:08 PM, David A Case <>
> wrote:
>> On Fri, Oct 06, 2017, Shirin Jamshidi wrote:
>> >
>> > I could go forward successfully as below, but finally
>> > I still couldn't run sander.MPI
>> ?? I don't see any error messages in the rest of your email.
>> > ./configure -mpi -cuda -openmp gnu
>> > make install
>> Note: with the -cuda switch, you only make pmemd.cuda.MPI (which you will
>> probably never use.) This command will not build sander.MPI. Get rid
>> of the -cuda and -openmp flags, and run configure and make install again.
>> ....dac
>> _______________________________________________
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Received on Fri Oct 06 2017 - 15:00:02 PDT
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