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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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Windows binary at Sourceforge #507

Closed thomas836 closed 6 years ago

thomas836 commented 6 years ago

Hi,

I tried to run the windows binary currently, however I noted, that APBS didn't use multithreading and only used 1 core out of 12 possibles of the CPU. Additionally, when I tried to run the parallel mg mode the program instantly crashed. This happened for the binaries of the 1.5, 1.4.1 and 1.4.2 build. The log file says, that the APBS version wasn't compiled with MPI in case for the mg-para. Is was wondering if there is any fix for this. Thanks a lot for your help.

Cheers

kozlac commented 6 years ago

Hello @fubula , we usually don't distribute the binaries with MPI support since not every system will have the necessary libraries or capabilities. For the multi-threading, that was on oversight. The compilation flag for multi-threading used to be enabled by default which changed at some point and we failed to noticed. I can create a binary with multi-thread support and let you know as soon as is up. However, if you need MPI I could try to help you walk through the steps for compiling a binary.

sobolevnrm commented 6 years ago

Hi @kozlac, please create the multi-thread support binary regardless. Thanks!

thomas836 commented 6 years ago

Hey,

sorry for bothering again, I was just wondering roughly when to expect the newly compiled binaries. Thanks a lot for your help.

Best, Thomas

On Oct 17, 2017, at 03:57, Nathan Baker notifications@github.com wrote:

Hi @kozlac https://github.com/kozlac, please create the multi-thread support binary regardless. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Electrostatics/apbs-pdb2pqr/issues/507#issuecomment-337094422, or mute the thread https://github.com/notifications/unsubscribe-auth/AX6_p7iLKffsdcA2Q8tLRy36YA4YTCHzks5stAl6gaJpZM4P6w19.

kozlac commented 6 years ago

@fubula I'm hoping to have it by tonight or tomorrow.

kozlac commented 6 years ago

@fubula, the windows binary with thread support is up. Thank you for your patience.