Dear Amber Users,
I am trying to do an averagelinkage clustering using ptraj cluster.
The scrpit for clustering is as follows:
#!/bin/sh
/soft/amber11/exe/ptraj 2zni.prm.top << EOF
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11000_11010.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11010_11020.crd
....
...
cluster out testcluster representative pdb \
average pdb averagelinkage clusters 12 rms sieve 10 .CA
Now when I use 11-12ns for clustering, the code work fine and I get the final
testcluster.txt output.
However, when I increase the no. of snapshots for clustering from 1000 to say
1500/2000 and above, the second pass of the clustering stops with the following
error:
******
PTRAJ CLUSTER: Clustering elapsed time: 596 seconds
Printing distribution of distances to file testcluster.txt
Distribution of Distances
[ 0.599, 0.644] -- 0.11% ( 12 out of 11175)
[ 0.644, 0.688] -- 0.46% ( 51 out of 11175)
[ 0.688, 0.733] -- 0.98% ( 109 out of 11175)
[ 0.733, 0.777] -- 2.09% ( 234 out of 11175)
[ 0.777, 0.822] -- 4.18% ( 467 out of 11175)
[ 0.822, 0.866] -- 7.52% ( 840 out of 11175)
[ 0.866, 0.911] -- 11.62% ( 1298 out of 11175)
[ 0.911, 0.955] -- 14.77% ( 1650 out of 11175)
[ 0.955, 1.000] -- 16.03% ( 1791 out of 11175)
[ 1.000, 1.044] -- 13.75% ( 1537 out of 11175)
[ 1.044, 1.089] -- 10.44% ( 1167 out of 11175)
[ 1.089, 1.133] -- 7.49% ( 837 out of 11175)
[ 1.133, 1.178] -- 4.76% ( 532 out of 11175)
[ 1.178, 1.222] -- 2.59% ( 289 out of 11175)
[ 1.222, 1.267] -- 1.57% ( 176 out of 11175)
[ 1.267, 1.311] -- 0.90% ( 101 out of 11175)
[ 1.311, 1.356] -- 0.33% ( 37 out of 11175)
[ 1.356, 1.400] -- 0.29% ( 32 out of 11175)
[ 1.400, 1.445] -- 0.09% ( 10 out of 11175)
[ 1.445, 1.489] -- 0.04% ( 5 out of 11175)
*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption
(!prev): 0x0000000002cbf500 ***
======= Backtrace: =========
/lib64/libc.so.6[0x310aa70412]
/lib64/libc.so.6(cfree+0x8c)[0x310aa73b1c]
/lib64/libc.so.6(fclose+0x14b)[0x310aa5f1eb]
/soft/amber11/exe/ptraj[0x4248f9]
/soft/amber11/exe/ptraj[0x4249f2]
/soft/amber11/exe/ptraj[0x424a18]
/soft/amber11/exe/ptraj[0x44b15f]
/soft/amber11/exe/ptraj[0x4538b1]
/soft/amber11/exe/ptraj[0x4397fb]
/soft/amber11/exe/ptraj[0x4045ea]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x310aa1dab4]
/soft/amber11/exe/ptraj(realloc+0x119)[0x4041f9]
======= Memory map: ========
00400000-00714000 r-xp 00000000 08:06 3240670
/soft/amber11/bin/ptraj
00913000-0091d000 rwxp 00313000 08:06 3240670
/soft/amber11/bin/ptraj
0091d000-04045000 rwxp 0091d000 00:00 0 [heap]
3109800000-310981a000 r-xp 00000000 08:03 554906
/lib64/ld-2.6.so
3109a1a000-3109a1b000 r-xp 0001a000 08:03 554906
/lib64/ld-2.6.so
3109a1b000-3109a1c000 rwxp 0001b000 08:03 554906
/lib64/ld-2.6.so
310aa00000-310ab47000 r-xp 00000000 08:03 554908
/lib64/libc-2.6.so
310ab47000-310ad47000 ---p 00147000 08:03 554908
/lib64/libc-2.6.so
310ad47000-310ad4b000 r-xp 00147000 08:03 554908
/lib64/libc-2.6.so
310ad4b000-310ad4c000 rwxp 0014b000 08:03 554908
/lib64/libc-2.6.so
310ad4c000-310ad51000 rwxp 310ad4c000 00:00 0
310ae00000-310ae82000 r-xp 00000000 08:03 555003
/lib64/libm-2.6.so
310ae82000-310b081000 ---p 00082000 08:03 555003
/lib64/libm-2.6.so
310b081000-310b082000 r-xp 00081000 08:03 555003
/lib64/libm-2.6.so
310b082000-310b083000 rwxp 00082000 08:03 555003
/lib64/libm-2.6.so
310b600000-310b615000 r-xp 00000000 08:03 554989
/lib64/libpthread-2.6.so
310b615000-310b814000 ---p 00015000 08:03 554989
/lib64/libpthread-2.6.so
310b814000-310b815000 r-xp 00014000 08:03 554989
/lib64/libpthread-2.6.so
310b815000-310b816000 rwxp 00015000 08:03 554989
/lib64/libpthread-2.6.so
310b816000-310b81a000 rwxp 310b816000 00:00 0
3118800000-311880d000 r-xp 00000000 08:03 554965
/lib64/libgcc_s-4.1.2-20070925.so.1
311880d000-3118a0d000 ---p 0000d000 08:03 554965
/lib64/libgcc_s-4.1.2-20070925.so.1
3118a0d000-3118a0e000 rwxp 0000d000 08:03 554965
/lib64/libgcc_s-4.1.2-20070925.so.1
2aaaaaaab000-2aaaaaaae000 rwxp 2aaaaaaab000 00:00 0
2aaaaaac8000-2aaaaab5e000 r-xp 00000000 08:05 2715247
/usr/lib64/libgfortran.so.1.0.0
2aaaaab5e000-2aaaaad5d000 ---p 00096000 08:05 2715247
/usr/lib64/libgfortran.so.1.0.0
2aaaaad5d000-2aaaaad5f000 rwxp 00095000 08:05 2715247
/usr/lib64/libgfortran.so.1.0.0
2aaaaad5f000-2aaaac26b000 rwxp 2aaaaad5f000 00:00 0
2aaab0000000-2aaab0021000 rwxp 2aaab0000000 00:00 0
2aaab0021000-2aaab4000000 ---p 2aaab0021000 00:00 0
2aaad0513000-2aaad1ec6000 rwxp 2aaad0513000 00:00 0
2aaad1ec7000-2aaad23ea000 rwxp 2aaad1ec7000 00:00 0
2aaad23eb000-2aaad267c000 rwxp 2aaad23eb000 00:00 0
2aaad267d000-2aaad290e000 rwxp 2aaad267d000 00:00 0
7fff0c4bf000-7fff0c4d4000 rwxp 7ffffffea000 00:00 0 [stack]
7fff0c5fd000-7fff0c600000 r-xp 7fff0c5fd000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
a2.sh: line 158: 23993 Aborted /soft/amber11/exe/ptraj
2zni.prm.top <<EOF
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11000_11010.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11010_11020.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11020_11030.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11030_11040.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11040_11050.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11050_11060.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11060_11070.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11070_11080.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11080_11090.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11090_11100.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11100_11110.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11110_11120.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11120_11130.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11130_11140.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11140_11150.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11150_11160.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11160_11170.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11170_11180.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11180_11190.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11190_11200.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11200_11210.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11210_11220.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11220_11230.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11230_11240.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11240_11250.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11250_11260.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11260_11270.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11270_11280.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11280_11290.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11290_11300.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11300_11310.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11310_11320.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11320_11330.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11330_11340.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11340_11350.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11350_11360.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11360_11370.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11370_11380.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11380_11390.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11390_11400.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11400_11410.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11410_11420.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11420_11430.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11430_11440.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11440_11450.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11450_11460.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11460_11470.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11470_11480.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11480_11490.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11490_11500.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11500_11510.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11510_11520.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11520_11530.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11530_11540.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11540_11550.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11550_11560.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11560_11570.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11570_11580.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11580_11590.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11590_11600.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11600_11610.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11610_11620.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11620_11630.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11630_11640.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11640_11650.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11650_11660.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11660_11670.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11670_11680.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11680_11690.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11690_11700.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11700_11710.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11710_11720.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11720_11730.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11730_11740.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11740_11750.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11750_11760.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11760_11770.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11770_11780.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11780_11790.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11790_11800.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11800_11810.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11810_11820.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11820_11830.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11830_11840.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11840_11850.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11850_11860.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11860_11870.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11870_11880.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11880_11890.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11890_11900.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11900_11910.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11910_11920.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11920_11930.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11930_11940.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11940_11950.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11950_11960.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11960_11970.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11970_11980.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11980_11990.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11990_12000.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12000_12010.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12010_12020.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12020_12030.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12030_12040.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12040_12050.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12050_12060.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12060_12070.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12070_12080.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12080_12090.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12090_12100.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12100_12110.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12110_12120.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12120_12130.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12130_12140.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12140_12150.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12150_12160.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12160_12170.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12170_12180.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12180_12190.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12190_12200.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12200_12210.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12210_12220.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12220_12230.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12230_12240.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12240_12250.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12250_12260.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12260_12270.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12270_12280.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12280_12290.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12290_12300.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12300_12310.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12310_12320.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12320_12330.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12330_12340.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12340_12350.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12350_12360.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12360_12370.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12370_12380.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12380_12390.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12390_12400.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12400_12410.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12410_12420.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12420_12430.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12430_12440.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12440_12450.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12450_12460.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12460_12470.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12470_12480.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12480_12490.crd
trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12490_12500.crd
cluster out testcluster representative pdb average pdb averagelinkage
clusters 12 rms sieve 10 .CA
EOF
******
Can you please tell me what is going wrong? I am using ambertools version 1.4
and during the "make test" there were no errors detected.
Thanks a lot in advance.
Sincere Regards,
Moitrayee
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Received on Fri Jul 09 2010 - 05:30:03 PDT
