Charm++ parallel programming system

["Choi, Jaemin" <jchoi157 AT illinois.edu>]

Hi Sutirtha,

Please let us know if the forwarded procedure solves the problem.

Thank you.

Jaemin Choi

Ph.D. Student, Research Assistant

Parallel Programming Laboratory

University of Illinois Urbana-Champaign

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From: prakash waghmode [prakash.waghamode AT gmail.com]
Sent: Thursday, August 10, 2017 12:37 PM
To: Choi, Jaemin
Subject: Re: [charm] FW: Problem with charm++ building

Building NAMD

In brief, the following steps are sufficient to build Namd and its dependent applications from the command line:

Part 1, FFTW: see building FFTW with a single change, use FFTW version(2.1.5)

Part 2, Charm++: see building Charm++

Part 3, NAMD: Now build the NAMD code.

Copy the file Linux-amd64-MPI-open64.archinto the arch subdirectory and then build NAMD.

Note: Linux-amd64-MPI-open64.archassumes that Charm++ was installed in $(HOME)/charm-5.9. If this is not the case, you need to modify CHARM_LOC in this file. The file Make.charm also needs to point to the directory where Charm++ is installed.

There is also an implicit assumption in the file arch/Linux-amd64.fftw that assumes FFTW was built in $(HOME)/fftw. If this is not true, you need to modify that file as well.

Now we continue as follows on command line:

     >cd ../namd_2.6

Then download the Linux-amd64-MPI-open64.arch file and copy to the archdirectory in namd_2.6. Also the Linux-amd64.fftw file should be copied to the same location,

     >./config fftw Linux-amd64-MPI-open64
     >cd Linux-amd64-MPI-open64
     >make

Known limitations

There is a bug in opencc such that if the serial C code in Charm++ is compiled with -O2 or higher, it will result in a hang during execution. The workaround is to use -O1 for CMK_SEQ_CC. This workaround is incorporated in the distributed conv-mach.sh, and seems to have no performance impact.

Prakash Waghmode

On 10-Aug-2017 10:39 PM, "Choi, Jaemin" <jchoi157 AT illinois.edu> wrote:

Can someone who've built NAMD before answer this question?

Thanks,

Jaemin Choi

Ph.D. Student, Research Assistant

Parallel Programming Laboratory

University of Illinois Urbana-Champaign

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From: sutirtha kamal sen [sks.silentnight AT gmail.com]
Sent: Saturday, August 05, 2017 2:41 AM
To: Choi, Jaemin
Subject: Re: [charm] Problem with charm++ building

oh! sorry, I must have missed them.

I followed the following line of instructions:

tar xf NAMD_2.11_Source.tar.gz
cd NAMD_2.11_Source
tar xf charm-6.7.0.tar
wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
tar xzf fftw-linux-x86_64.tar.gz
mv linux-x86_64 fftw
tar xzf tcl*-linux-x86_64.tar.gz
tar xzf tcl*-linux-x86_64-threaded.tar.gz
mv tcl*-linux-x86_64 tcl
mv tcl*-linux-x86_64-threaded tcl-threaded
cd charm-6.7.0
./build charm++  verbs-linux-x86_64 gcc --with-production

In first try, they were showing some indiband/verbs.h missing; then when I corrected that, a string of other errors in various machine.c and related files

On Fri, Aug 4, 2017 at 10:10 PM, Choi, Jaemin <jchoi157 AT illinois.edu> wrote:

Hi Sutirtha,

Could you tell us what the build command was?
Also, the attachments seem to be missing.

Thanks,



Jaemin Choi
Ph.D. Student, Research Assistant
Parallel Programming Laboratory
University of Illinois Urbana-Champaign

________________________________________
From: sutirtha kamal sen [sks.silentnight AT gmail.com]
Sent: Friday, August 04, 2017 1:45 AM
To: charm AT cs.illinois.edu
Subject: [charm] Problem with charm++ building

Hello
I am having problems with building of charm++. Apparently, a file named "infiniband/verbs.h" is missing in the package due to which the build is not executed completely. Even if I make the program ignore that include statement, I'm getting a string of errors due to which the build is terminated. I am getting the errors, as given in the files attached error_1 and error_2 respectively. Please check the problems and look into it.I will be obliged.

Thanking You,
Sutirtha Kamal Sen