Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Sun, 18 Jul 2010 09:37:47 -0400

I have a new patch that fixes the gzip issue. This patch supersedes
the patch 'ptraj_2010-07-08-fixEndian.patch'.

Before applying this patch, if you have already applied the
'ptraj_2010-07-08-fixEndian.patch' you must remove it by copying the
attached backup.io.c to $AMBERHOME/AmberTools/src/ptraj/io.c.

Instructions for applying this patch are located at the head of the
patch file. Let me know if there are any issues with the patch.

-Dan

> On Fri, Jun 25, 2010 at 7:55 PM, Paul S. Nerenberg <psn.berkeley.edu> wrote:
>> Hi all,
>>
>> I recompiled AmberTools 1.4 today after applying the latest bugfixes
>> and this seems to have somehow broken ptraj's ability to analyze
>> gzipped trajectory files.  When running "make test", this build passed
>> everything fine (zero reported errors), but I'm not sure what, if any,
>> compressed trajectories are encountered by ptraj during those tests.
>> Here is the typical error message I get upon opening a gzipped
>> trajectory:
>>
>> PTRAJ: trajin ./mdcrd/ala3_wat_prod2_s1.mdcrd.gz
>>   Checking coordinates: ./mdcrd/ala3_wat_prod2_s1.mdcrd.gz
>>        Could not process trajectory ./mdcrd/ala3_wat_prod2_s1.mdcrd.gz
>> ...eventually dies due to no input trajectory...
>>
>> If I first gunzip any of these trajectories myself, however, it reads
>> and analyzes the uncompressed trajectories with no problem (although
>> it does gives the "there is a problem" output):
>>
>> PTRAJ: trajin ./mdcrd/ala3_wat_prod2_s1.mdcrd
>>   Checking coordinates: ./mdcrd/ala3_wat_prod2_s1.mdcrd
>> checkCoordinates(): Could not predict number of frames for AMBER
>> trajectory file: ./mdcrd/ala3_wat_prod2_s1.mdcrd
>>        If this is not a compressed file then there is a problem
>> Rank: 0 Atoms: 2396 FrameSize: 58248 TitleSize: 81 NumBox: 3 Seekable 0
>> ...snip...
>> PTRAJ: Successfully read the input file.
>>        Coordinate processing will occur until EOF (unknown number of
>> frames).
>>        Summary of I/O and actions follows:
>> ...lots of output...
>>
>> If I go back to the original AmberTools 1.4 source code (i.e., no
>> bugfixes) and recompile, then ptraj reads both compressed and
>> uncompress trajectories just fine:
>>
>> [compressed...yes, this does look the same as the uncompressed above]
>> PTRAJ: trajin ./mdcrd/ala3_wat_prod2_s1.mdcrd.gz
>>   Checking coordinates: ./mdcrd/ala3_wat_prod2_s1.mdcrd.gz
>> checkCoordinates(): Could not predict number of frames for AMBER
>> trajectory file: ./mdcrd/ala3_wat_prod2_s1.mdcrd.gz
>>        If this is not a compressed file then there is a problem
>> Rank: 0 Atoms: 2396 FrameSize: 58248 TitleSize: 81 NumBox: 3 Seekable 0
>> ...snip...
>> PTRAJ: Successfully read the input file.
>>        Coordinate processing will occur until EOF (unknown number of
>> frames).
>>        Summary of I/O and actions follows:
>> ...lots of output...
>>
>> OR
>>
>> [uncompressed]
>> PTRAJ: trajin ./mdcrd/ala3_wat_prod2_s1.mdcrd
>>   Checking coordinates: ./mdcrd/ala3_wat_prod2_s1.mdcrd
>> Rank: 0 Atoms: 2396 FrameSize: 58248 TitleSize: 81 NumBox: 3 Seekable 1
>> ...snip...
>> PTRAJ: Successfully read the input file.
>>        Coordinate processing will occur on 50000 frames.
>>        Summary of I/O and actions follows:
>> ...lots of output...
>>
>>
>> Altogether this behavior suggests to me that bugfix.4 may have
>> actually broken something (else) with compressed trajectory files.
>> Post-bugfix.4, it appears to be acting like compressed files are
>> garbage and uncompressed files are compressed, while pre-bugfix.4, the
>> behavior is normal.  Have any others noticed similar problems since
>> applying bugfix.4?
>>
>> Thanks,
>>
>> Paul
>>
>> P.S. Just some details on my system: MacOS 10.5.8 (dual Xeon machine),
>> gcc 4.5.0 (rev 4), and the latest versions of gmp, gperf, mpfr,
>> libmpc, etc. available from MacPorts.
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
-- 
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854




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Received on Sun Jul 18 2010 - 07:00:03 PDT
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