Hi,
This was caused by a bug in the clustering code. The file stack was
not being cleared properly when an output cluster trajectory became
too large, which led to a double free and a segfault. Please apply the
attached patch and recompile;
cd $AMBERHOME
patch -p0 -N < patchfile
Let me know if this solves the issue for you.
-Dan
On Mon, Oct 4, 2010 at 9:11 AM, Senthil Natesan <sen.natesan.yahoo.com> wrote:
> I just installed AmberTools1.4 a few days ago and I applied all bugfixes as of
> that day.
>
> thanks,
>
> Senthil
>
>
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Mon, October 4, 2010 7:50:42 AM
> Subject: Re: [AMBER] ptraj- cluster analysis - Error
>
> What version of Ptraj are you using, and have you applied the bugfixes?
>
> -Dan
>
> On Sun, Oct 3, 2010 at 1:15 PM, Senthil Natesan <sen.natesan.yahoo.com> wrote:
>>
>> I have run ptraj cluster analysis on 1ns MD trajectory. Everything seemed fine
>> but the at the end
>>
>> the following error message was thrown to the terminal. I could see all out
> put
>> files, successfully written,
>> but I am afraid because of these messages. Can someone please suggest me what
>>is
>> going on?
>>
>>---------------------------------------------------------------------------------------------------------------
>>-
>>
>> PTRAJ: Processing input from "STDIN" ...
>>
>> PTRAJ: trajin ../b0101cxmd4.mdcrd
>> Checking coordinates: ../b0101cxmd4.mdcrd
>> Rank: 0 Atoms: 31851 FrameSize: 774005 TitleSize: 81 NumBox: 3 Seekable 1
>>
>>
>> PTRAJ: cluster out b0101md all amber representative pdb average pdb
>> averagelinkage sieve 5 clusters 4 rms mass ":25-28, 46-48, 93-97, 146-148,
>> 161-162, 300"
>>
>> MASK = :25-28, 46-48, 93-97, 146-148, 161-162, 300
>> Mask [:25-28, 46-48, 93-97, 146-148, 161-162, 300] represents 284 atoms
>> [No output trajectory specified (trajout)]
>> ../b0101cxmd4.mdcrd: 5000 frames.
>>
>> PTRAJ: Successfully read the input file.
>> Coordinate processing will occur on 5000 frames.
>> Summary of I/O and actions follows:
>>
>> INPUT COORDINATE FILES
>> File (../b0101cxmd4.mdcrd) is an AMBER trajectory (with box info) with 5000
>> sets
>>
>> NO OUTPUT COORDINATE FILE WAS SPECIFIED
>>
>> ACTIONS
>> 1> CLUSTERING.
>>
>> Clusters will be assigned and output to files with the prefix "b0101md".
>> The clustering algorithm is AverageLink using RMS as the distance metric.
>> Cluster-to-cluster distance is measured by its centroid.
>> The cluster count is set to 4.
>> Clustering will be performed in two passes (sieve method).
>> Sieved frames in the first pass will be selected every 5 frames starting
>> from frame 1.
>> The atom selection for best fit is
>> :25-28,:46-48,:93-97,:146-148,:161,:162,:300
>> Output of type 'all' will be written to a file of type: 'Amber
> trajectory'
>> Output of type 'representative' will be written to a file of type: 'PDB'
>> Output of type 'average' will be written to a file of type: 'PDB'
>>
>>
>> Processing AMBER trajectory file ../b0101cxmd4.mdcrd
>>
>> 1% ............ 25% ............ 50% ............ 75% ............ 100%
>>
>>
>> The first pass through the trajectory is complete.
>> Read in the existing PairwiseDistances file
>> Clustering using the average linkage algorithm.
>> Aligning the most representative frames from each clusters to cluster 2.
>> Sieve was active. Preparing for the second pass.
>> Dumping out current clusters to file EndFirstPass.txt.
>> Clustering elapsed time: 86 seconds
>> Computing centroids and expanding clusters.
>> Ready for the second pass through the trajectories...
>>
>> Processing AMBER trajectory file ../b0101cxmd4.mdcrd
>>
>> 1% ............ 25% ............ 50% ............ 75% ............ 100%
>>
>>
>> PTRAJ: Successfully read in 5000 sets and processed 5000 sets.
>>
>> Dumping accumulated results (if any)
>>
>>
>> PTRAJ CLUSTER: Clustering elapsed time: 516 seconds
>> Printing distribution of distances to file b0101md.txt
>> Distribution of Distances
>> [ 0.365, 0.424] -- 0.02% ( 87 out of 499500)
>> [ 0.424, 0.483] -- 0.28% ( 1374 out of 499500)
>> [ 0.483, 0.542] -- 1.64% ( 8186 out of 499500)
>> [ 0.542, 0.601] -- 5.12% ( 25596 out of 499500)
>> [ 0.601, 0.660] -- 10.27% ( 51277 out of 499500)
>> [ 0.660, 0.719] -- 14.25% ( 71200 out of 499500)
>> [ 0.719, 0.779] -- 14.71% ( 73459 out of 499500)
>> [ 0.779, 0.838] -- 13.14% ( 65642 out of 499500)
>> [ 0.838, 0.897] -- 11.77% ( 58778 out of 499500)
>> [ 0.897, 0.956] -- 9.94% ( 49669 out of 499500)
>> [ 0.956, 1.015] -- 7.46% ( 37284 out of 499500)
>> [ 1.015, 1.074] -- 5.11% ( 25543 out of 499500)
>> [ 1.074, 1.133] -- 3.15% ( 15741 out of 499500)
>> [ 1.133, 1.192] -- 1.76% ( 8802 out of 499500)
>> [ 1.192, 1.252] -- 0.84% ( 4188 out of 499500)
>> [ 1.252, 1.311] -- 0.36% ( 1818 out of 499500)
>> [ 1.311, 1.370] -- 0.12% ( 609 out of 499500)
>> [ 1.370, 1.429] -- 0.04% ( 194 out of 499500)
>> [ 1.429, 1.488] -- 0.01% ( 41 out of 499500)
>> [ 1.488, 1.547] -- 0.00% ( 12 out of 499500)
>> *** glibc detected *** ptraj: double free or corruption (!prev):
>> 0x00000000127d99e0 ***
>> ======= Backtrace: =========
>> /lib64/libc.so.6[0x3d53c71ce2]
>> /lib64/libc.so.6(cfree+0x8c)[0x3d53c7590c]
>> /lib64/libc.so.6(fclose+0x14b)[0x3d53c60d0b]
>> ptraj[0x4229e9]
>> ptraj[0x422ae2]
>> ptraj[0x422b08]
>> ptraj[0x449771]
>> ptraj[0x451f85]
>> ptraj[0x437cbf]
>> ptraj[0x4026da]
>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x3d53c1d974]
>> ptraj[0x4022e9]
>> ======= Memory map: ========
>> 00400000-00557000 r-xp 00000000 00:1a 93135736
>> /home/tripos/amber11_install/amber11/bin/ptraj
>> 00757000-00761000 rw-p 00157000 00:1a 93135736
>> /home/tripos/amber11_install/amber11/bin/ptraj
>> 00761000-00765000 rw-p 00761000 00:00 0
>> 11ae2000-130b3000 rw-p 11ae2000 00:00 0
> [heap]
>> 3d53800000-3d5381c000 r-xp 00000000 08:01 2148192
>> /lib64/ld-2.5.so
>> 3d53a1b000-3d53a1c000 r--p 0001b000 08:01 2148192
>> /lib64/ld-2.5.so
>> 3d53a1c000-3d53a1d000 rw-p 0001c000 08:01 2148192
>> /lib64/ld-2.5.so
>> 3d53c00000-3d53d4c000 r-xp 00000000 08:01 2148193
>> /lib64/libc-2.5.so
>> 3d53d4c000-3d53f4c000 ---p 0014c000 08:01 2148193
>> /lib64/libc-2.5.so
>> 3d53f4c000-3d53f50000 r--p 0014c000 08:01 2148193
>> /lib64/libc-2.5.so
>> 3d53f50000-3d53f51000 rw-p 00150000 08:01 2148193
>> /lib64/libc-2.5.so
>> 3d53f51000-3d53f56000 rw-p 3d53f51000 00:00 0
>> 3d55000000-3d55082000 r-xp 00000000 08:01 2147955
>> /lib64/libm-2.5.so
>> 3d55082000-3d55281000 ---p 00082000 08:01 2147955
>> /lib64/libm-2.5.so
>> 3d55281000-3d55282000 r--p 00081000 08:01 2147955
>> /lib64/libm-2.5.so
>> 3d55282000-3d55283000 rw-p 00082000 08:01 2147955
>> /lib64/libm-2.5.so
>> 3d55c00000-3d55c0d000 r-xp 00000000 08:01 2148203
>> /lib64/libgcc_s-4.1.2-20080825.so.1
>> 3d55c0d000-3d55e0d000 ---p 0000d000 08:01 2148203
>> /lib64/libgcc_s-4.1.2-20080825.so.1
>> 3d55e0d000-3d55e0e000 rw-p 0000d000 08:01 2148203
>> /lib64/libgcc_s-4.1.2-20080825.so.1
>> 2b992e179000-2b992e17b000 rw-p 2b992e179000 00:00 0
>> 2b992e185000-2b992e186000 rw-p 2b992e185000 00:00 0
>> 2b992e186000-2b992e21c000 r-xp 00000000 08:01 3325914
>> /usr/lib64/libgfortran.so.1.0.0
>> 2b992e21c000-2b992e41b000 ---p 00096000 08:01 3325914
>> /usr/lib64/libgfortran.so.1.0.0
>> 2b992e41b000-2b992e41d000 rw-p 00095000 08:01 3325914
>> /usr/lib64/libgfortran.so.1.0.0
>> 2b992e41d000-2b992ea54000 rw-p 2b992e41d000 00:00 0
>> 2b9930000000-2b9930021000 rw-p 2b9930000000 00:00 0
>> 2b9930021000-2b9934000000 ---p 2b9930021000 00:00 0
>> 2b9945b7d000-2b9945f4f000 rw-p 2b9945b7d000 00:00 0
>> 2b9945f50000-2b994647d000 rw-p 2b9945f50000 00:00 0
>> 2b994647e000-2b99466b6000 rw-p 2b994647e000 00:00 0
>> 7fff7c91b000-7fff7c930000 rw-p 7ffffffea000 00:00 0
>> [stack]
>> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
> [vdso]
>> ./as1.sh: line 2: 2629 Aborted
>>--------------------------------------------------------------------------------------------
>>-
>>
>>
>>
>> thanks,
>>
>> Senthil Natesan
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 07 2010 - 14:30:03 PDT
