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
>
>
>
>
> _______________________________________________
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>
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Received on Mon Oct 04 2010 - 06:30:03 PDT
