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#35012 - 05/26/15 10:47 AM Patch files
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 15
The purpose of this thread is to index patch files for CHARMM releases.
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Josh Buckner
Brooks Lab
University of Michigan

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#35013 - 05/26/15 11:01 AM Re: Patch files [Re: bucknerj]
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 15
Relevant Reports:
Redmine Issue 171
Forum Post 34977 (c39b1 openmm single-gpu)

Description:
This patch is to correct a memory leak in the OpenMM-related code for SVN branch c39b. The patch can be applied to SVN revision 369.

Version Compatibility
The patch file is known to work with CHARMM versions
c39b1 and c39b2
and OpenMM 6.1 and 6.2.0

Instructions:
Apply the patch from CHARMM root with 'patch -p0 < patch.txt', and then compile/install CHARMM as usual.


Attachments
patch.txt (355 downloads)



Edited by bucknerj (05/28/15 04:12 PM)
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Josh Buckner
Brooks Lab
University of Michigan

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#35014 - 05/26/15 11:17 AM Re: Patch files [Re: bucknerj]
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 15
Relevant Reports
Redmine Issue 156
Forum Post 34977 (c39b1 openmm dual-gpu)

Description
This patch is to correct high temps/energies seen using CHARMM/OpenMM with multiple GPUs. It can be applied to SVN branch c39b revision 369.

This patch is compatible only with OpenMM versions 6.1 and 6.2

Some users report minimal performance gains (10% - 20%) using multiple GPUs. In addition, some testcases still fail after patching:

The following test cases still report energies that look suspicious and self-report failure. They all make heavy use of OpenMM's CustomNonbondedForce.
c38test/omm_block-periodic2.out
c38test/omm_block-periodic.out
c38test/omm_switch-nbfix.out
c38test/omm_switch.out

OpenMM's GBSAOBC does not yet support multi-gpu and so this testcase throws an apt C++ exception.
c40test/omm_gbsaobc_stream-test.out

Apply this patch only if you absolutely insist on using multiple gpus per CHARMM session.

Version Compatibility
The patch file is known to work with CHARMM versions
c39b1 and c39b2
and OpenMM 6.1 and 6.2.0


Instructions
Apply the patch from CHARMM root with 'patch -p0 < patch.txt', and then compile/install CHARMM as usual.


Attachments
patch.txt (411 downloads)



Edited by bucknerj (05/28/15 04:13 PM)
_________________________
Josh Buckner
Brooks Lab
University of Michigan

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#36198 - 01/26/17 03:16 PM Re: Patch files [Re: bucknerj]
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 15
Relevant Reports:
Redmine Issue 181

Description:
When doing a minimization with BLOCK and PME the EWKSum energy explodes after 2-3 steps. This only happens with non-parallel code. With parallel code, even if running on a single node, it works fine.

Version Compatibility
This patch file is known to work with c41b and trunk branches of the CHARMM SVN at commit 579.

Instructions:
Apply the patch from CHARMM root with 'patch -p0 < patch.txt', and then compile/install CHARMM as usual.



Attachments
patch.txt (219 downloads)



Edited by bucknerj (01/26/17 03:17 PM)
_________________________
Josh Buckner
Brooks Lab
University of Michigan

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#36260 - 02/16/17 04:42 PM Re: Patch files [Re: bucknerj]
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 15
Description:
There was a problem with recompiling an openmm build after the first compile with install.com

Also, copying the charmm executable, moving the lib directory or moving OpenMM caused only the Reference platform to be available.

Now when you move the library, plugin directories or executable, you
can set LD_LIBRARY_PATH, OPENMM_PLUGIN_DIR, and CHARMM_PLUGIN_DIR

At runtime, be sure to add OPENMM_PLUGIN_DIR and CHARMM_PLUGIN_DIR to LD_LIBRARY_PATH
just to make sure everything is linked correctly.

If you don't move anything after installation, you shouldn't have to
set OPENMM_PLUGIN_DIR or CHARMM_PLUGIN_DIR.

Version Compatibility
This patch file only works with c41b2.

Instructions:
Apply the patch from CHARMM root with 'patch -p0 < patch.txt', and then compile/install CHARMM as usual.


Attachments
patch.txt (312 downloads)

_________________________
Josh Buckner
Brooks Lab
University of Michigan

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#36272 - 02/24/17 03:34 PM Re: Patch files [Re: bucknerj]
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 15
Description:
This patch fixes mpi deadlocks that may occur after building with gcc 6 and doing
dyna 0 nstep ...
with more than one node (in parallel).

This patch also fixes a problem with ?dmc being undefined in the test script c41test/ndmc.inp in builds with gcc 6 and runs with more than one node (in parallel).

Version Compatibility
This patch file works with c41b2 and c42a2

Instructions:
Apply the patch from CHARMM root with 'patch -p0 < patch.txt', and then compile/install CHARMM as usual.


Attachments
patch.txt (168 downloads)

_________________________
Josh Buckner
Brooks Lab
University of Michigan

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#36274 - 02/27/17 11:29 AM Re: Patch files [Re: bucknerj]
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 15
Description:
This patch fixes the first derivatives from 'test first ...' in c41test/ndmc.inp and is related to the dmc energy term.

Version Compatibility
This patch file works with c41b2 and c42a2

Instructions:
Apply the patch from CHARMM root with 'patch -p0 < patch.txt', and then compile/install CHARMM as usual.


Attachments
patch.txt (154 downloads)

_________________________
Josh Buckner
Brooks Lab
University of Michigan

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#37174 - 10/19/18 05:22 PM Re: Patch files [Re: bucknerj]
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 15
Description
This patch fixes the sccdftb build for install.com
IE install.com <host> T ...
If you are using
configure --with-sccdftb ...
you do not need this patch.

Version Compatibility
This patch is for c43b1 and c44a1

Instructions
Apply the patch from CHARMM source root with
patch -p1 < patch.txt
and then use install.com as usual.


Attachments
patch.txt (55 downloads)

_________________________
Josh Buckner
Brooks Lab
University of Michigan

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