Questions about the MPIRUN

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Libnag
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Questions about the MPIRUN

Post by Libnag » 19 May 2015, 11:35

Dear everyone,

Recently, i installed the Dalton-2015 in UBUNTU 14.04 (64 bit) with use of the gfortran 4.8.2 and openmpi 1.6.5, both the serial and parallel version are compiled successfully.
Unfortunately, i found there are four output files generated when i used the order: mpirun -np 4 dalton x.dal. x.mol. Moreover, the Total CPU time used in parallel nearly two times of serial.
The Dalton code is compiled by this order:
cd dalton
./setup mpi
cd mpi
make

Any suggestions are welcome.

olav
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Re: Questions about the MPIRUN

Post by olav » 19 May 2015, 11:50

You should do

./setup --mpi

What you have now is a serial build in a subdirectory with the name mpi/.

Regards,
Olav

taylor
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Re: Questions about the MPIRUN

Post by taylor » 19 May 2015, 13:00

In addition to what Olav has said, I recommend also you should not try to run the dalton.x executable in the way you are doing. There is a script called

Code: Select all

dalton
in the same directory and this is what you should use to run the code. It is capable of invoking Dalton in both a serial and a parallel fashion (and it's quite well documented in the manual...)

I should add that there are expert Dalton users who know how to set up the necessary scratch directories, copy the necessary files, etc., to run dalton.x directly. The fact that you had difficulties with the build (the --mpi parameter) suggests to me that you probably do not have so much experience with Dalton to run this way, which is why I recommend you use the script.

Best regards
Pete

ljr.argentina
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Re: Questions about the MPIRUN

Post by ljr.argentina » 19 May 2015, 15:42

Hi, the site www.openmpi.org suggests installing the new version 1.8.5, which can be downloaded from the same site.
There have in the FAQ section for installation help.
you have to do ./setup --mpi, once you've installed the OpenMPI bookstores, and you have declared in $ PATH and $ LD_LIBRARY_PATH

Leopoldo.

taylor
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Re: Questions about the MPIRUN

Post by taylor » 19 May 2015, 16:15

The OpenMPI version is not the problem. The problem is two-fold: the user did not in fact build against the OpenMPI libraries, and also should not be running the program directly. The dalton runscript is much safer except for very expert users. This script will execute the appropriate mpirun commands.

In general I strongly recommend people do not go with the latest version of OpenMPI (and indeed most things) the moment it is released. At my supercomputer centre in Melbourne we would routinely build and test the latest release internally, and install it but not announce it (we used modules as the mechanism for users to modify their initial configuration) until all the dust had settled around issues that invariably arise.

Best regards
Pete

Libnag
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Re: Questions about the MPIRUN

Post by Libnag » 20 May 2015, 03:46

Thanks for all the suggestions, as olav said, i re-compiled the code and the Dalton runs well.
Actually, i am a newbie of Dalton, i will pay more attention on the manual first.

Best
Yubing

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