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Multiple times printed output while using MPI
#37836 04/14/20 02:14 PM
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pmj Offline OP
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Hi!

I was trying to install a parallel version of CHARMM on another machine. I usually do it with:

./install.com gnu M

I get this printed on the screen:

install.com> Processing CHARMM source on gnu...

Using mpif90 for compile
ar: `u' modifier ignored since `D' is the default (see `U')

The binary is there and it runs, but I get each line printed 16 times for each node I am using in the output file.

How can I fix this issue?

Thank you

Re: Multiple times printed output while using MPI
pmj #37837 04/14/20 04:17 PM
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rmv Offline
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There is likely an issue with the input script being used; the most common cause is changing PRNLEV or WRNLEV w/o restricting the change to initial process with the [optional] NODE 0 argument.


Rick Venable
computational chemist

Re: Multiple times printed output while using MPI
rmv #37838 04/14/20 06:42 PM
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pmj Offline OP
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Thank you, Rick. I did not use PRNLEV or WRNLEV. I just noticed that depending on the machine I am using, the scripts are the same, but on some, I get this multi printed output for some reason. Is there any way to fix this? Does that mean, the binary that you get is faulty or it works fine?

Re: Multiple times printed output while using MPI
pmj #37839 04/14/20 07:30 PM
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CHARMM version? Compiler version(s) used? Machine types and OS versions? Name of the MPI library and version(s)? Is this a test case or your own script? If your own, can you attach it as a .txt file? Have you run the test case suite?


Rick Venable
computational chemist

Re: Multiple times printed output while using MPI
rmv #37873 05/10/20 06:58 PM
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pmj Offline OP
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Dear Rick,

so I am using c42b2 version. I already have it installed on multiple machines, but the one I cannot seem to fix and not to have the multiple printed output is on

Linux node25 4.9.0-6-amd64 #1 SMP Debian 4.9.82-1+deb9u3 (2018-03-02) x86_64 GNU/Linux

It is my script I was using on another machine with the same version of Charmm.

When I am trying to install it here I get the following:

install.com> Directory /work/paula/Software/c42b2/build/gnu_M does not exist.
Creating /work/paula/Software/c42b2/build/gnu_M ...

install.com> Phase 1 completed.

install.com> The preprocessor prefx_gnu installed.

install.com> Phase 2 completed.

install.com> Processing CHARMM source on gnu...

Using mpif90 for compile
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')

I am not sure how to fix this. It seems there is the same error even if I try to compile the serial version.
Best
Paula

Last edited by pmj; 05/10/20 07:01 PM.
Re: Multiple times printed output while using MPI
pmj #37874 05/10/20 08:11 PM
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The message from 'ar' is harmless and can be ignored. I was able to build a non-parallel version w/ o problems on an Ubuntu system; I got the same message about ar, but the build completed.

Code
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
 
 install.com> CHARMM Installation is completed.
              The CHARMM executable is /u/rvenable/Charmm/c42b2/exec/gnu/charmm.
 
 install.com> Phase 3 completed.
Sun May 10 15:51:23 EDT 2020

I cannot test the parallel build easily, as we use CentOS for our compute nodes, and all of our MPI libraries have been built on those machines, and there are some subtle differences between Debian-based Linux (like Ubuntu) and RedHat-based Linux (such as CentOS). I don't see any errors here.

Note that with the gnu compiler, any MPI library used must be built with the same compiler version used to build CHARMM.


Rick Venable
computational chemist

Re: Multiple times printed output while using MPI
rmv #37875 05/11/20 07:36 AM
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pmj Offline OP
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Dear Rick,

I was actually just wondering what this 'ar' mistake and is it a big issue, so thanks.

thanks for checking. I will see if the libraries were built with the same compiler. Since I am not in charge of the machines, but just a user I am not sure whether was used.

Best
Paula

Re: Multiple times printed output while using MPI
pmj #37876 05/11/20 04:15 PM
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What is most important is the mpi.mod file, which provides the Fortran90 interface for the MPI implementation; in my experience, the build has failed when mpi.mod was created with a different gfortran version than the one being used to compile CHARMM.


Rick Venable
computational chemist


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