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testfiles for c35b2 failed
#20573 03/30/09 10:03 AM
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Dear all,

I am having some trouble with the test files for my charmm build (version c35b2).
I build charmm with the gfortran-4.1 compiler and openmpi-1.2.8 using:

./install.com gnu medium M MPISPECIAL x86_64 GFORTRAN

I then downloaded the c35b1_gf_64.tar.gz file which, so I understood, is the right one for my charmm version.

Using the provided test.com, I ran all tests and then running

awk -f compare.awk -v verbose=0 -v tol=0.01 170309.rpt

produced about 50% failures.

Unfortunately, the documentation which is on the CD is completly outdated and one has to hunt for information of how to install and test charmm. So anybody saying now: RTFM will get the reply from me: get me a version of the manual which is acutally up to date. Sorry, but I had to air my frustation here as for a commercial product I found that outrages.

Nonetheless, could anybody point me in the direction what is going on here?

All the best

Jörg

Re: testfiles for c35b2 failed
sassy #20574 03/30/09 04:28 PM
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You are correct; the documentation is badly out of date, and is among the worst of any such program with the stature of CHARMM.

You should start by comparing single processor test results, w/o MPI

You should probably compare to to c35b2 instead of c35b1

I also suggest upgrading to a more recent gfortran version

Re: testfiles for c35b2 failed
rmv #20575 04/16/09 02:34 PM
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Daer RMV,

thanks for the reply, and sorry for my delayed response.

Updating gfortran sounds like a good idea, however, that would mean updating the whole cluster or building your own gfortran. I do not really want to do either for various reasons

I am doing the build for a single CPU now, see if that goes any better. Unfortunately, I seem to be unable to use the ifort version I have to build the binary. I get problems related to the code during compilation.

As for the test suite, I only found c35b1_gf_64 that which was apparently build on a 64bit platform. I would love to use the c35b2_gf_32 but not only was that build on a 32bit platform, it also uses the 4.2.x gfortran compiler. So here I have changed 2 different parameters.

For a commercial product I find it astonishing not to provdie a reliable test suite.

I will try the singe build and see how it goes.

All the best

Jörg

Re: testfiles for c35b2 failed
sassy #20576 04/16/09 03:33 PM
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CHARMM is academic software, written and maintained by post-docs, grad students, and working scientists on a strictly volunteer basis; it is an evolving academic research tool, certainly not commercial software. There are commercial entanglements with Accelrys, who re-packages the software as CHARMm, which is one reason an academic license fee is required; CHARMM cannot be made freely available.

There are known issues with gfortran compilers earlier than 4.1.2; caveat emptor. There have been some reports of problems with ifort 10.x as well. In our lab, with a centrally mounted software repository for the cluster, we have multiple compilers available; we recommend gfortran 4.3.x and Intel 11.x for CHARMM. With the central repository, there's no need to update cluster nodes to roll out a new compiler.

Re: testfiles for c35b2 failed
sassy #20577 04/16/09 03:54 PM
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I can't help noticing that you repeatedly refer to CHARMM as "a commercial product". This is not quite true. CHARMM development is driven by a number of academic groups all over the world. It is a sad truth that we get funded for publishing research papers but not for writing documentation, making our software user-friendly, removing bugs that don't affect the majority of users, or providing support on these very forums. We all do this purely as a community service. If you want to fund a full-time Ph.D. level employee for improving CHARMM's user-friendliness (which, admittedly, is astonishingly low), I'm sure you would make everyone in the CHARMM community very happy. Otherwise, I respectfully urge you to drop the "dissatisfied customer" tone; it won't make you many friends here.

Just for the sake of completeness, I should mention that the company Accelrys does sell a minimally modified version of CHARMM as a commercial product branded CHARMm. If that's what you're using, you could try the "dissatisfied customer" thing with them. Perhaps someone down the line might one day decide to pour some of the profits generated by CHARMm sales into improving CHARMM's user-friendliness.

Edit: oops, rmv beat me to it.

Last edited by Kenno; 04/16/09 03:56 PM.
Re: testfiles for c35b2 failed
Kenno #20578 04/17/09 10:29 AM
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Dear Kenno,

I may quote from the website: "We distribute the source code of the CHARMM program with documentation to individual academic research groups for a $600 licensing fee."
As soon as I pay money for something it is a commercial product in my humble opinion. There are codes which are completly free and they offer an up to date documentation, in some instances even right down to the acutal version you are using, _including_ new features etc.

They are doing that on a volunteer base as well and it works, so I don't see any reason why CHARMM is not able to do that. Writing software you want to distribute also means writing manuals, else you get frustrating people like me. I am not getting paid searching the internet for information of a product I am paying money for.

Sorry for being upfront here. One can do better and I would have thougth that Harvad as one of the IV-leagues could afford somebody to write the documentation of their product they are selling.

All the best

Jörg

Re: testfiles for c35b2 failed
sassy #20579 04/17/09 05:07 PM
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I for one haven't seen any of that money, and I doubt that anyone on this forum has. Nobody here is very happy with CHARMM's current level of user-friendliness and documentation, but we're powerless to change it. You might be right to complain, but you're complaining to the wrong people. Maybe you should direct your complaints through the same channels as you directed your money...

Re: testfiles for c35b2 failed
Kenno #20580 04/17/09 06:04 PM
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One reason people like me spend time answering questions in the forum is the knowledge that the documentation is far from good, and people often need some additional guidance. This has led to correcting some errors in the .doc file, and some fixes to install.com among other things.

One problem is that NIH and NSF grants typically don't cover things like improving program documentation, and the principal scientists involved often don't have the resources to support a documentation and packaging improvement project.

Re: testfiles for c35b2 failed
rmv #20581 04/17/09 06:38 PM
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If we should try to keep things a little bit in perspective:

1. There is really no money at all to speak about (in terms of a large-scale software project) floating around from the academic CHARMM license fee.

2. This thread started with a question about failing testcases. The testcases are being modernized to be self-contained and thus useful for end-users. At present they are best used by developers to make sure that code modifications do not break existing functionality. Many testcases unfortunately use procedures (eg, long simulations) that give slightly different results with different compilers; I think this is what you see. Since CHARMM has very many testcases it will take time to get all this modernized. Anybody is welcome to contribute to this task, and to improving the documentation.

3. User friendliness. Well? The underlying concepts are complicated, and this is software for very complicated tasks (the baseline for this statement is ab initio calculations), and it is a research tool. Very flexible and versatile. It does take time to learn to use it, and to understand what is going on. This is true for all advanced MD software. For "user-friendliness" there are several simple frontends, allowing a more narrow set of tasks to be performed easily: CHARMM-GUI,MMTSB,CHARMMING, Discovery Studio and PipelinePilot, and doubtless many others. A very simple task, running a modernized version of the first protein MD simulation of BPTI (McCammon, Gelin & Karplus (1977 Nature) can be done with this set of commands, and I do not think this is unfriendly at all:
* 10ps dynamics of BPTI in vacuum
*
READ rtf card name top_all22_prot.inp
READ param card name par_all22_prot.inp
READ sequence pdb name bpti.pdb ! bpti pbd file with just BPTI
GENErate bpti
PATCh disu bpti 5 bpti 55
PATCh disu bpti 14 bpti 38
PATCh disu bpti 30 bpti 51
READ coor pdb name bpti.pdb
HBUIld select hydrogen end
shake bonds
OPEN unit 11 write unformatted name bpti.trj
DYNAmics start nstep 10000 timestep 0.001 –
firsttemp 35.0 finaltemp 285.0 teminc 50.0 ihtfrq 200 -
cutnb 14.0 ctofnb 12.0 fshift inbfrq -1 nsavc 100 iuncrd 11

OPEN unit 11 read unformatted name bpti.trj
COOR dyna firstunit 11 nunits 1
WRITe coor pdb name bpti-ave.pdb
* Averaged coordinates. RMS fluctuations in B-factor column
*

I would also like to suggest that starting with simple tasks, and looking carefully at the examples in the Script Archive, is a good way to begin using CHARMM and get started on what admittedly is an uphill learning curve.

Specific questions and suggestions are always welcome.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: testfiles for c35b2 failed
lennart #20582 04/17/09 10:26 PM
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Added consideration. A move towards increased "user-friendliness" (most users are already very friendly though) would be much helped by a clear definition of "user-friendliness". If we are striving towards something like:
charmm < PDB_ID > manuscript.pdf -jif acceptable_journal_impact_factor
then the default for -jif could probably not be extremely impressive; for more information about impact factors see also Genome Biology 2008, 9:107 (doi:10.1186/gb-2008-9-7-107).


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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