Charm++ parallel programming system

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

Another suggestion is to drop the "gcc" option in your build command (like 
Nitin's).
It could currently cause the build to use a version of gcc in a non-default 
path.

Thanks,

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

________________________________________
From: Bhat, Nitin
Sent: Thursday, August 10, 2017 1:19 PM
To: Choi, Jaemin; 
sks.silentnight AT gmail.com
Cc: 
charm AT cs.illinois.edu
Subject: Re: [charm] FW: Problem with charm++ building

Hi Sutirtha,

From your error files, it looks like you’re trying to build a verbs build of 
Charm++ on a machine where Infiniband Verbs (a network layer software 
package) is not installed. Which machine are you trying to build Charm++ on? 
Is this a local linux machine (like a laptop or a desktop) or a 
cluster/supercomputer with Infiniband network?

If it’s a cluster (or a supercomputer) with Infiniband network, you can ask 
your System Administrator to install Verbs and then build Charm++ on top of 
that using your original build command (./build charm++  verbs-linux-x86_64 
gcc --with-production).

If it’s a local machine or any other cluster without a proprietary network 
(like Infiniband interconnect), you can use another build of Charm++ like 
netlrts: ./build charm++ netlrts-linux-x86_64  --with-production. 
Additionally, if MPI is installed on the machine, you can also build Charm on 
top of MPI: ./build charm++ mpi-linux-x86_64 –with-production.

After building Charm++ successfully, the instructions in notes.txt should be 
sufficient to help you build NAMD.

Thanks,
Nitin

From: "Choi, Jaemin" 
<jchoi157 AT illinois.edu>
Reply-To: "Choi, Jaemin" 
<jchoi157 AT illinois.edu>
Date: Thursday, August 10, 2017 at 12:55 PM
To: 
"sks.silentnight AT gmail.com"
 
<sks.silentnight AT gmail.com>
Cc: 
"charm AT cs.illinois.edu"
 
<charm AT cs.illinois.edu>
Subject: [charm] FW: Problem with charm++ building

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
________________________________
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<https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.amd.com_wordpress_media_2012_10_building-5Ffftw.html&d=DwMFAw&c=8hUWFZcy2Z-Za5rBPlktOQ&r=x3NNBo1sW-0Ro900LIARhw_4yZMfh7AfgFTrqQHfc5M&m=vzZQorcCfBqNgzoshc4f9h7trUi3QBhiy_ZchExm7uk&s=AxmfQyspAQdF3oMj3e_kkdxpOYevUSAnkBgPTzocYOc&e=>
 with a single change, use FFTW version(2.1.5)

Part 2, Charm++: see building 
Charm++<https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.amd.com_wordpress_media_2012_10_building-5Fcharmpp.html&d=DwMFAw&c=8hUWFZcy2Z-Za5rBPlktOQ&r=x3NNBo1sW-0Ro900LIARhw_4yZMfh7AfgFTrqQHfc5M&m=vzZQorcCfBqNgzoshc4f9h7trUi3QBhiy_ZchExm7uk&s=57U7EpDtx09FdM1LE7KQM9tMK-xNNbStLroMWEk5Pgg&e=>

Part 3, NAMD: Now build the NAMD code.

Copy the file 
Linux-amd64-MPI-open64.arch<https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.amd.com_wordpress_media_2012_10_Linux-2Damd64-2DMPI-2Dopen64.arch&d=DwMFAw&c=8hUWFZcy2Z-Za5rBPlktOQ&r=x3NNBo1sW-0Ro900LIARhw_4yZMfh7AfgFTrqQHfc5M&m=vzZQorcCfBqNgzoshc4f9h7trUi3QBhiy_ZchExm7uk&s=Wf4jXaEUoFCfqynHFm5eLyR6rsAvMya6GxG-VveqI58&e=>into
 the arch subdirectory and then build NAMD.

Note: 
Linux-amd64-MPI-open64.arch<https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.amd.com_wordpress_media_2012_10_Linux-2Damd64-2DMPI-2Dopen64.arch&d=DwMFAw&c=8hUWFZcy2Z-Za5rBPlktOQ&r=x3NNBo1sW-0Ro900LIARhw_4yZMfh7AfgFTrqQHfc5M&m=vzZQorcCfBqNgzoshc4f9h7trUi3QBhiy_ZchExm7uk&s=Wf4jXaEUoFCfqynHFm5eLyR6rsAvMya6GxG-VveqI58&e=>assumes
 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.amd.com_wordpress_media_2012_10_Linux-2Damd64-2DMPI-2Dopen64.arch&d=DwMFAw&c=8hUWFZcy2Z-Za5rBPlktOQ&r=x3NNBo1sW-0Ro900LIARhw_4yZMfh7AfgFTrqQHfc5M&m=vzZQorcCfBqNgzoshc4f9h7trUi3QBhiy_ZchExm7uk&s=Wf4jXaEUoFCfqynHFm5eLyR6rsAvMya6GxG-VveqI58&e=>
 file and copy to the archdirectory in namd_2.6. Also the 
Linux-amd64.fftw<https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.amd.com_wordpress_media_2012_10_Linux-2Damd64.fftw&d=DwMFAw&c=8hUWFZcy2Z-Za5rBPlktOQ&r=x3NNBo1sW-0Ro900LIARhw_4yZMfh7AfgFTrqQHfc5M&m=vzZQorcCfBqNgzoshc4f9h7trUi3QBhiy_ZchExm7uk&s=HuBmod-h-sOg_c6p3e78lSBURDxhFYblGOoh8LCGYt0&e=>
 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<mailto: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
________________________________
From: sutirtha kamal sen 
[sks.silentnight AT gmail.com<mailto: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<mailto: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<mailto:sks.silentnight AT gmail.com>]
Sent: Friday, August 04, 2017 1:45 AM
To: 
charm AT cs.illinois.edu<mailto: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