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Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
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difficulty reading from fastsearch index #966

Open openbabel-bot opened 14 years ago

openbabel-bot commented 14 years ago

This problem was originally posted on openbabel-discuss forum by David Rose-9 on Nov. 15, 2007. However, I still have exactly the same problem using version 2.2.3, which is the last one on Feb. 19, 2010, on my x86 64 bit RedHat Linux and it is better to notice the problem here.

I have had several instances where I build a fast search index without any apparent trouble but then can't search it without an error. I finally have a small example of this problem that I can post, using a 10 molecule smi file (ten.smi) as input:

$ cat ten.smi C12(C(N(C(=O)C)c3c2cccc3)=O)Nc2c(ccc(c2N1)OCCCC)OCCCC n1c([nH]c(cc1c1ccccc1)=O)c1ccc(cc1)Br n1c(nc2c(c1N(C)C)cccc2)c1c(O)cccc1 C1(/[CH]2[CH]3\C(=C4/CC(C)(C)NC(C4)(C)C)C=C[CH]3[CH]1C=C2)=C1/CC(C)(C)NC(C1)(C)C n1c(c2ccc(C(=O)O)cc2)ccc(c1)CCCCC N1(C(CN(CC1=O)C(=O)C1CCCCC1)=O)CCc1ccccc1 S(N1CHC#N)(c1ccc(cc1)C)(=O)=O c12c(c(OC)c3c(c1OC)occ3)ccc(o2)=O c12c(OCHC(C)C)cc1c(c2)ccc(=O)o1 c12[C]3([C@H]4(N@@CC@HC3))C(=O)OC

file looks OK...build index:

$ babel ten.smi -ofs This will prepare an index of ten.smi and may take some time... It took 0 seconds 10 molecules converted 37 audit log messages

$ ls -lt ten.fs -rw-r--r-- 1 rose staff 1564 Nov 15 12:51 ten.fs

looks OK, no errors, fs file exists and has stuff in it. Try a search:

$ babel ten.fs -ifs -s'Nc2nc(c1ccccc1)nc3ccccc23' out.smi ============================== *** Open Babel Error in ReadChemObject Difficulty reading from index ten.fs

0 molecules converted 1 errors 1 audit log messages

From this past post ---Problem using fs index file--- (http://n4.nabble.com/Problem-using-fs-index-file-td958832.html#a958832), problem may be caused by incompatible binary operation on 64 bit machine but I cannot figure out the cause.

Reported by: makio323

openbabel-bot commented 14 years ago

ten.smi input SMILES file

Original comment by: makio323

openbabel-bot commented 14 years ago

Works fine on 64-bit Windows. Strangely though, only 2 molecules are converted either with 32-bit or 64-bit:

C:\Tools\openbabel\trunk\windows-vc2008\build64\Release>babel ten.smi -ofs This will prepare an index of ten.smi and may take some time... It contains 10 molecules It took 0 seconds 2 molecules converted 31 audit log messages

Original comment by: @baoilleach

openbabel-bot commented 14 years ago

I also see only 2 molecules converted on 32bit Windows (with the development code). But the problem is data dependent and intermittent. Apparently irrelevant changes during debugging can make the problem go away and the read position in the input file apparently moves erratically. So an over-writing or alignment problem looks probable. The header is binary but its interpretation in C++ makes assumptions about how a C++ struct is laid out - clearly not a good idea. I have in the past written a version with the header in ASCII but did not proceed because correcting another bug seemed to solve the problem.

It seems likely that the bug is a more general I/O on the header and not confined to 64bit systems. I'll try revising the header reading and writing code. In the longer term I would like fastsearch files to be portable binary in Andrew Dalke's FPB format, if it ever comes to fruition.

Original comment by: @chrismorl

openbabel-bot commented 14 years ago

The incomplete reading problem reported by Noel was that ALL_READS_BINARY had not been set by CMake build. (It is now done in the code.) Without it, seekg() gave incorrect results with UNIX file endings under MSVC.

In revision 3556 in the trunk code the binary read and write of header variables in fs files are done separately, to avoid the possibility that a struct is laid out differently on other platforms. Maybe this will cure the problem on Linux 64 bit systems?

Original comment by: @chrismorl

openbabel-bot commented 14 years ago

That's great Chris. I'll follow this up again. Let me know if you want me to edit the CMake build.

Original comment by: @baoilleach

openbabel-bot commented 14 years ago

Just tested latest dev code on a 64bit Linux system. Seems to work fine:

babel ten.fs -ifs -s'Nc2nc(c1ccccc1)nc3ccccc23' out.smi 1 candidates from fingerprint search phase 1 molecule converted

makeio, could you test the development code and see whether the problem has gone away for you. See the instructions at http://openbabel.org/wiki/CMake 1 info messages 57 audit log messages

Original comment by: nobody

openbabel-bot commented 14 years ago

Added a test for this to the test suite (testfastsearch.py). It passes on a variety of 64-bit and 32-bit systems (http://my.cdash.org/testSummary.php?project=57&name=pytest_fastsearch&date=2010-03-01), so I'm marking this as pending. The failures are the systems where all of the tests fail and are not specific to this test.

This will close automatically in 2 weeks unless reopened by the original submitter.

Original comment by: @baoilleach

openbabel-bot commented 14 years ago

I encounter another problem during working the developmental code on March 1st. I follow the instruction of the CMake (http://openbabel.org/wiki/CMake) OpenBabel to compile the development code on RedHad Linux of 64bit box.

First, the newly compiled babel program fails making an index output file as follows.

$ babel ten.smi -osf

babel: cannot write output format!

Open Babel 2.2.99 -- Mar 1 2010 -- 15:53:14

Usage: babel [-i] [-o]

Try -H option for more information.

However, it can convert the SMILES file into a SDF file without any problem by “babel -ismi ten.smi -osdf ten.sdf”. Yes, it can write SDF output, but not index....

Second, during the “make test”, some tests failed as follows:

Running tests...

Test project path/to/build/openbabel

  Start  1: uniqueid_Test

1/37 Test #1: uniqueid_Test .................... Passed 0.01 sec

  Start  2: smiles_Test

2/37 Test #2: smiles_Test ......................***Exception: SegFault 0.04 sec

  Start  3: stereo_Test

3/37 Test #3: stereo_Test ......................***Exception: SegFault 0.04 sec

  Start  4: tetrahedral_Test

4/37 Test #4: tetrahedral_Test ................. Passed 0.00 sec

  Start  5: tetranonplanar_Test

5/37 Test #5: tetranonplanar_Test .............. Passed 0.00 sec

  Start  6: tetraplanar_Test

6/37 Test #6: tetraplanar_Test ................. Passed 0.00 sec

  Start  7: cistrans_Test

7/37 Test #7: cistrans_Test ....................***Exception: SegFault 0.02 sec

  Start  8: stereoperception_Test

8/37 Test #8: stereoperception_Test ............ Passed 0.03 sec

  Start  9: aromatest_Test

9/37 Test #9: aromatest_Test ...................***Exception: SegFault 0.03 sec

  Start 10: atom_Test

10/37 Test #10: atom_Test ........................ Passed 0.00 sec

  Start 11: bond_Test

11/37 Test #11: bond_Test ........................ Passed 0.00 sec

  Start 12: cansmi_Test

12/37 Test #12: cansmi_Test ...................... Passed 1.27 sec

  Start 13: cmlreadfile_Test

13/37 Test #13: cmlreadfile_Test ................. Passed 0.02 sec

  Start 14: conversion_Test

14/37 Test #14: conversion_Test .................. Passed 0.01 sec

  Start 15: datatest_Test

15/37 Test #15: datatest_Test .................... Passed 0.00 sec

  Start 16: ffghemical_Test

16/37 Test #16: ffghemical_Test ..................***Failed 0.01 sec

  Start 17: ffmmff94_Test

17/37 Test #17: ffmmff94_Test ....................***Failed 0.01 sec

  Start 18: ffuff_Test

18/37 Test #18: ffuff_Test .......................***Failed 0.01 sec

  Start 19: formalcharge_Test

19/37 Test #19: formalcharge_Test ................ Passed 0.12 sec

  Start 20: format_Test

20/37 Test #20: format_Test ...................... Passed 0.01 sec

  Start 21: formula_Test

21/37 Test #21: formula_Test ..................... Passed 0.21 sec

  Start 22: internalcoord_Test

22/37 Test #22: internalcoord_Test ............... Passed 0.00 sec

  Start 23: invalidsmarts_Test

23/37 Test #23: invalidsmarts_Test ............... Passed 0.00 sec

  Start 24: invalidsmiles_Test

24/37 Test #24: invalidsmiles_Test ............... Passed 0.01 sec

  Start 25: iterators_Test

25/37 Test #25: iterators_Test ................... Passed 0.13 sec

  Start 26: logp_psa_Test

26/37 Test #26: logp_psa_Test ....................***Exception: SegFault 0.02 sec

  Start 27: math_Test

27/37 Test #27: math_Test ........................ Passed 0.13 sec

  Start 28: mol_Test

28/37 Test #28: mol_Test ......................... Passed 0.02 sec

  Start 29: phmodel_Test

29/37 Test #29: phmodel_Test .....................***Exception: SegFault 0.05 sec

  Start 30: residue_Test

30/37 Test #30: residue_Test ..................... Passed 0.03 sec

  Start 31: ringtest_Test

31/37 Test #31: ringtest_Test .................... Passed 0.13 sec

  Start 32: smartstest_Test

32/37 Test #32: smartstest_Test .................. Passed 0.21 sec

  Start 33: smilesmatch_Test

33/37 Test #33: smilesmatch_Test .................***Exception: SegFault 1.44 sec

  Start 34: unitcell_Test

34/37 Test #34: unitcell_Test .................... Passed 0.00 sec

  Start 35: pytest_babel

35/37 Test #35: pytest_babel .....................***Failed 0.03 sec

  Start 36: pytest_sym

36/37 Test #36: pytest_sym ....................... Passed 0.08 sec

  Start 37: pytest_fastsearch

37/37 Test #37: pytest_fastsearch ................***Failed 0.03 sec

68% tests passed, 12 tests failed out of 37

Total Test time (real) = 4.23 sec

The following tests FAILED:

  2 - smiles_Test (SEGFAULT)

  3 - stereo_Test (SEGFAULT)

  7 - cistrans_Test (SEGFAULT)

  9 - aromatest_Test (SEGFAULT)

 16 - ffghemical_Test (Failed)

 17 - ffmmff94_Test (Failed)

 18 - ffuff_Test (Failed)

 26 - logp_psa_Test (SEGFAULT)

 29 - phmodel_Test (SEGFAULT)

 33 - smilesmatch_Test (SEGFAULT)

 35 - pytest_babel (Failed)

 37 - pytest_fastsearch (Failed)

Makio

Original comment by: makio323

openbabel-bot commented 14 years ago

Your first problem on March 1st could be a typo: should be -ofs

Original comment by: @chrismorl

openbabel-bot commented 14 years ago

The issue with the tests is simply that you need to set some environment variables. I'll write them up on the wiki tomorrow - Noel

Original comment by: @baoilleach

openbabel-bot commented 14 years ago

If you use CMake 2.8, and rerun the configure step, "make test" should work better now.

Original comment by: @baoilleach

openbabel-bot commented 14 years ago

Yes, it was my typo and it indeed makes an index file without any problem. The substructure search in the original example seems to work fine but it produces a bunch of message as follows.

I am using CMake 2.8.0 and recompile OpenBabel today in case there may be some changes in codes. However, I encounter the same error messages during the “make test” process. Once Noel update the wiki, I will set up environments and test it.

Makio

$ babel ten.fs -ifs -s'Nc2nc(c1ccccc1)nc3ccccc23' out.smi 1 candidates from fingerprint search phase

1 molecule converted

1 info messages 57 audit log messages

glibc detected babel: double free or corruption (!prev): 0x000000000755ed10 ***

======= Backtrace: =========

/lib64/libc.so.6[0x3cd4a722ef]

/lib64/libc.so.6(cfree+0x4b)[0x3cd4a7273b]

/path/to/local/lib/libopenbabel.so.4[0x2b0dae442328]

/path/to/local/lib/libopenbabel.so.4[0x2b0dae5e6164]

/lib64/libc.so.6(__cxa_finalize+0x8e)[0x3cd4a3368e]

/path/to/local/lib/libopenbabel.so.4[0x2b0dae43ee56]

======= Memory map: ========

00400000-00405000 r-xp 00000000 fd:00 30900304 /path/to/local/bin/babel

00605000-00606000 rw-p 00005000 fd:00 30900304 /path/to/local/bin/babel

07516000-07610000 rw-p 07516000 00:00 0

3cd4600000-3cd461c000 r-xp 00000000 fd:00 90997106 /lib64/ld-2.5.so

3cd481b000-3cd481c000 r--p 0001b000 fd:00 90997106 /lib64/ld-2.5.so

3cd481c000-3cd481d000 rw-p 0001c000 fd:00 90997106 /lib64/ld-2.5.so

3cd4a00000-3cd4b4d000 r-xp 00000000 fd:00 90997107 /lib64/libc-2.5.so

3cd4b4d000-3cd4d4d000 ---p 0014d000 fd:00 90997107 /lib64/libc-2.5.so

3cd4d4d000-3cd4d51000 r--p 0014d000 fd:00 90997107 /lib64/libc-2.5.so

3cd4d51000-3cd4d52000 rw-p 00151000 fd:00 90997107 /lib64/libc-2.5.so

3cd4d52000-3cd4d57000 rw-p 3cd4d52000 00:00 0

3cd4e00000-3cd4e82000 r-xp 00000000 fd:00 90997114 /lib64/libm-2.5.so

3cd4e82000-3cd5081000 ---p 00082000 fd:00 90997114 /lib64/libm-2.5.so

3cd5081000-3cd5082000 r--p 00081000 fd:00 90997114 /lib64/libm-2.5.so

3cd5082000-3cd5083000 rw-p 00082000 fd:00 90997114 /lib64/libm-2.5.so

3cd5200000-3cd5202000 r-xp 00000000 fd:00 90997115 /lib64/libdl-2.5.so

3cd5202000-3cd5402000 ---p 00002000 fd:00 90997115 /lib64/libdl-2.5.so

3cd5402000-3cd5403000 r--p 00002000 fd:00 90997115 /lib64/libdl-2.5.so

3cd5403000-3cd5404000 rw-p 00003000 fd:00 90997115 /lib64/libdl-2.5.so

3cd5e00000-3cd5e14000 r-xp 00000000 fd:00 98973122 /usr/lib64/libz.so.1.2.3

3cd5e14000-3cd6013000 ---p 00014000 fd:00 98973122 /usr/lib64/libz.so.1.2.3

3cd6013000-3cd6014000 rw-p 00013000 fd:00 98973122 /usr/lib64/libz.so.1.2.3

3cdd800000-3cdd933000 r-xp 00000000 fd:00 98966221 /usr/lib64/libxml2.so.2.6.26

3cdd933000-3cddb33000 ---p 00133000 fd:00 98966221 /usr/lib64/libxml2.so.2.6.26

3cddb33000-3cddb3c000 rw-p 00133000 fd:00 98966221 /usr/lib64/libxml2.so.2.6.26

3cddb3c000-3cddb3d000 rw-p 3cddb3c000 00:00 0

3ce3c00000-3ce3c0d000 r-xp 00000000 fd:00 90996797 /lib64/libgcc_s-4.1.2-20080825.so.1

3ce3c0d000-3ce3e0d000 ---p 0000d000 fd:00 90996797 /lib64/libgcc_s-4.1.2-20080825.so.1

3ce3e0d000-3ce3e0e000 rw-p 0000d000 fd:00 90996797 /lib64/libgcc_s-4.1.2-20080825.so.1

3ce6000000-3ce60e6000 r-xp 00000000 fd:00 98991952 /usr/lib64/libstdc++.so.6.0.8

3ce60e6000-3ce62e5000 ---p 000e6000 fd:00 98991952 /usr/lib64/libstdc++.so.6.0.8

3ce62e5000-3ce62eb000 r--p 000e5000 fd:00 98991952 /usr/lib64/libstdc++.so.6.0.8

3ce62eb000-3ce62ee000 rw-p 000eb000 fd:00 98991952 /usr/lib64/libstdc++.so.6.0.8

3ce62ee000-3ce6300000 rw-p 3ce62ee000 00:00 0

2b0dae3e5000-2b0dae3e6000 rw-p 2b0dae3e5000 00:00 0

2b0dae404000-2b0dae405000 rw-p 2b0dae404000 00:00 0

2b0dae405000-2b0dae652000 r-xp 00000000 fd:00 30968839 /path/to/local/lib/libopenbabel.so.4.0.0

2b0dae652000-2b0dae852000 ---p 0024d000 fd:00 30968839 /path/to/local/lib/libopenbabel.so.4.0.0

2b0dae852000-2b0dae85b000 rw-p 0024d000 fd:00 30968839 /path/to/local/lib/libopenbabel.so.4.0.0

2b0dae85b000-2b0dae89a000 rw-p 2b0dae85b000 00:00 0

2b0dae89a000-2b0dae8a1000 r-xp 00000000 fd:00 30968868 /path/to/local/lib/openbabel/2.2.99/jaguarformat.so

2b0dae8a1000-2b0daeaa0000 ---p 00007000 fd:00 30968868 /path/to/local/lib/openbabel/2.2.99/jaguarformat.so

2b0daeaa0000-2b0daeaa1000 rw-p 00006000 fd:00 30968868 /path/to/local/lib/openbabel/2.2.99/jaguarformat.so

2b0daeaa1000-2b0daeb8e000 r-xp 00000000 fd:00 30968935 /path/to/local/lib/libinchi.so.0.2.1

2b0daeb8e000-2b0daed8d000 ---p 000ed000 fd:00 30968935 /path/to/local/lib/libinchi.so.0.2.1

2b0daed8d000-2b0daeda3000 rw-p 000ec000 fd:00 30968935 /path/to/local/lib/libinchi.so.0.2.1

2b0daeda3000-2b0daedab000 r-xp 00000000 fd:00 30968928 /path/to/local/lib/openbabel/2.2.99/rsmiformat.so

2b0daedab000-2b0daefab000 ---p 00008000 fd:00 30968928 /path/to/local/lib/openbabel/2.2.99/rsmiformat.so

2b0daefab000-2b0daefac000 rw-p 00008000 fd:00 30968928 /path/to/local/lib/openbabel/2.2.99/rsmiformat.so

2b0daefac000-2b0daefb2000 r-xp 00000000 fd:00 30968882 /path/to/local/lib/openbabel/2.2.99/alchemyformat.so

2b0daefb2000-2b0daf1b1000 ---p 00006000 fd:00 30968882 /path/to/local/lib/openbabel/2.2.99/alchemyformat.so

2b0daf1b1000-2b0daf1b2000 rw-p 00005000 fd:00 30968882 /path/to/local/lib/openbabel/2.2.99/alchemyformat.so

2b0daf1b2000-2b0daf1bb000 r-xp 00000000 fd:00 30968871 /path/to/local/lib/openbabel/2.2.99/nwchemformat.so

2b0daf1bb000-2b0daf3ba000 ---p 00009000 fd:00 30968871 /path/to/local/lib/openbabel/2.2.99/nwchemformat.so

2b0daf3ba000-2b0daf3bb000 rw-p 00008000 fd:00 30968871 /path/to/local/lib/openbabel/2.2.99/nwchemformat.so

2b0daf3bb000-2b0daf3c0000 r-xp 00000000 fd:00 30968912 /path/to/local/lib/openbabel/2.2.99/msmsformat.so

2b0daf3c0000-2b0daf5bf000 ---p 00005000 fd:00 30968912 /path/to/local/lib/openbabel/2.2.99/msmsformat.so

2b0daf5bf000-2b0daf5c0000 rw-p 00004000 fd:00 30968912 /path/to/local/lib/openbabel/2.2.99/msmsformat.so

2b0daf5c0000-2b0daf5c6000 r-xp 00000000 fd:00 30968911 /path/to/local/lib/openbabel/2.2.99/msiformat.so

2b0daf5c6000-2b0daf7c5000 ---p 00006000 fd:00 30968911 /path/to/local/lib/openbabel/2.2.99/msiformat.so

2b0daf7c5000-2b0daf7c6000 rw-p 00005000 fd:00 30968911 /path/to/local/lib/openbabel/2.2.99/msiformat.so

2b0daf7c6000-2b0daf7ce000 r-xp 00000000 fd:00 30968880 /path/to/local/lib/openbabel/2.2.99/PQSformat.so

2b0daf7ce000-2b0daf9cd000 ---p 00008000 fd:00 30968880 /path/to/local/lib/openbabel/2.2.99/PQSformat.so

2b0daf9cd000-2b0daf9ce000 rw-p 00007000 fd:00 30968880 /path/to/local/lib/openbabel/2.2.99/PQSformat.so

2b0daf9ce000-2b0daf9de000 r-xp 00000000 fd:00 30968864 /path/to/local/lib/openbabel/2.2.99/gausscubeformat.so

2b0daf9de000-2b0dafbdd000 ---p 00010000 fd:00 30968864 /path/to/local/lib/openbabel/2.2.99/gausscubeformat.so

2b0dafbdd000-2b0dafbde000 rw-p 0000f000 fd:00 30968864 /path/to/local/lib/openbabel/2.2.99/gausscubeformat.so

2b0dafbde000-2b0dafbe4000 r-xp 00000000 fd:00 30968909 /path/to/local/lib/openbabel/2.2.99/mpdformat.so

2b0dafbe4000-2b0dafde3000 ---p 00006000 fd:00 30968909 /path/to/local/lib/openbabel/2.2.99/mpdformat.so

2b0dafde3000-2b0dafde4000 rw-p 00005000 fd:00 30968909 /path/to/local/lib/openbabel/2.2.99/mpdformat.so

2b0dafde4000-2b0dafdeb000 r-xp 00000000 fd:00 30968853 /path/to/local/lib/openbabel/2.2.99/pngformat.so

2b0dafdeb000-2b0daffea000 ---p 00007000 fd:00 30968853 /path/to/local/lib/openbabel/2.2.99/pngformat.so

2b0daffea000-2b0daffeb000 rw-p 00006000 fd:00 30968853 /path/to/local/lib/openbabel/2.2.99/pngformat.so

2b0daffeb000-2b0dafff5000 r-xp 00000000 fd:00 30968932 /path/to/local/lib/openbabel/2.2.99/pubchem.so

2b0dafff5000-2b0db01f4000 ---p 0000a000 fd:00 30968932 /path/to/local/lib/openbabel/2.2.99/pubchem.so

2b0db01f4000-2b0db01f5000 rw-p 00009000 fd:00 30968932 /path/to/local/lib/openbabel/2.2.99/pubchem.so

2b0db01f5000-2b0db0200000 r-xp 00000000 fd:00 30968906 /path/to/local/lib/openbabel/2.2.99/mmcifformat.so

2b0db0200000-2b0db03ff000 ---p 0000b000 fd:00 30968906 /path/to/local/lib/openbabel/2.2.99/mmcifformat.so

2b0db03ff000-2b0db0401000 rw-p 0000a000 fd:00 30968906 /path/to/local/lib/openbabel/2.2.99/mmcifformat.so

2b0db0401000-2b0db0407000 r-xp 00000000 fd:00 30968860 /path/to/local/lib/openbabel/2.2.99/dmolformat.so

2b0db0407000-2b0db0606000 ---p 00006000 fd:00 30968860 /path/to/local/lib/openbabel/2.2.99/dmolformat.so

2b0db0606000-2b0db0607000 rw-p 00005000 fd:00 30968860 /path/to/local/lib/openbabel/2.2.99/dmolformat.so

2b0db0607000-2b0db060f000 r-xp 00000000 fd:00 30968923 /path/to/local/lib/openbabel/2.2.99/xyzformat.so

2b0db060f000-2b0db080f000 ---p 00008000 fd:00 30968923 /path/to/local/lib/openbabel/2.2.99/xyzformat.so

2b0db080f000-2b0db0810000 rw-p 00008000 fd:00 30968923 /path/to/local/lib/openbabel/2.2.99/xyzformat.so

2b0db0810000-2b0db0816000 r-xp 00000000 fd:00 30968892 /path/to/local/lib/openbabel/2.2.99/chem3dformat.so

2b0db0816000-2b0db0a16000 ---p 00006000 fd:00 30968892 /path/to/local/lib/openbabel/2.2.99/chem3dformat.so

2b0db0a16000-2b0db0a17000 rw-p 00006000 fd:00 30968892 /path/to/local/lib/openbabel/2.2.99/chem3dformat.so

2b0db0a17000-2b0db0a18000 r-xp 00000000 fd:00 30968929 /path/to/local/lib/openbabel/2.2.99/xtcformat.so

2b0db0a18000-2b0db0c17000 ---p 00001000 fd:00 30968929 /path/to/local/lib/openbabel/2.2.99/xtcformat.so

2b0db0c17000-2b0db0c18000 rw-p 00000000 fd:00 30968929 /path/to/local/lib/openbabel/2.2.99/xtcformat.so

2b0db0c18000-2b0db0c1b000 r-xp 00000000 fd:00 30968849 /path/to/local/lib/openbabel/2.2.99/copyformat.so

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2b0db764a000-2b0db7651000 r-xp 00000000 fd:00 30968888 /path/to/local/lib/openbabel/2.2.99/cacaoformat.so

2b0db7651000-2b0db7850000 ---p 00007000 fd:00 30968888 /path/to/local/lib/openbabel/2.2.99/cacaoformat.so

2b0db7850000-2b0db7851000 rw-p 00006000 fd:00 30968888 /path/to/local/lib/openbabel/2.2.99/cacaoformat.so

2b0db7851000-2b0db785e000 r-xp 00000000 fd:00 30968870 /path/to/local/lib/openbabel/2.2.99/mopacformat.so

2b0db785e000-2b0db7a5e000 ---p 0000d000 fd:00 30968870 /path/to/local/lib/openbabel/2.2.99/mopacformat.so

2b0db7a5e000-2b0db7a5f000 rw-p 0000d000 fd:00 30968870 /path/to/local/lib/openbabel/2.2.99/mopacformat.so

2b0db7a5f000-2b0db7a6b000 r-xp 00000000 fd:00 30968916 /path/to/local/lib/openbabel/2.2.99/pqrformat.so

2b0db7a6b000-2b0db7c6a000 ---p 0000c000 fd:00 30968916 /path/to/local/lib/openbabel/2.2.99/pqrformat.so

2b0db7c6a000-2b0db7c6b000 rw-p 0000b000 fd:00 30968916 /path/to/local/lib/openbabel/2.2.99/pqrformat.so

2b0db7c6b000-2b0db7c73000 r-xp 00000000 fd:00 30968933 /path/to/local/lib/openbabel/2.2.99/xmlformat.so

2b0db7c73000-2b0db7e73000 ---p 00008000 fd:00 30968933 /path/to/local/lib/openbabel/2.2.99/xmlformat.so

2b0db7e73000-2b0db7e74000 rw-p 00008000 fd:00 30968933 /path/to/local/lib/openbabel/2.2.99/xmlformat.so

2b0db7e74000-2b0db7e91000 r-xp 00000000 fd:00 30968844 /path/to/local/lib/openbabel/2.2.99/smilesformat.so

2b0db7e91000-2b0db8091000 ---p 0001d000 fd:00 30968844 /path/to/local/lib/openbabel/2.2.99/smilesformat.so

2b0db8091000-2b0db8092000 rw-p 0001d000 fd:00 30968844 /path/to/local/lib/openbabel/2.2.99/smilesformat.so

2b0db8092000-2b0db809a000 r-xp 00000000 fd:00 30968896 /path/to/local/lib/openbabel/2.2.99/crkformat.so

2b0db809a000-2b0db8299000 ---p 00008000 fd:00 30968896 /path/to/local/lib/openbabel/2.2.99/crkformat.so

2b0db8299000-2b0db829a000 rw-p 00007000 fd:00 30968896 /path/to/local/lib/openbabel/2.2.99/crkformat.so

2b0db829a000-2b0db829f000 r-xp 00000000 fd:00 30968884 /path/to/local/lib/openbabel/2.2.99/amberformat.so

2b0db829f000-2b0db849f000 ---p 00005000 fd:00 30968884 /path/to/local/lib/openbabel/2.2.99/amberformat.so

2b0db849f000-2b0db84a0000 rw-p 00005000 fd:00 30968884 /path/to/local/lib/openbabel/2.2.99/amberformat.so

2b0db84a0000-2b0db84a5000 r-xp 00000000 fd:00 30968900 /path/to/local/lib/openbabel/2.2.99/featformat.so

2b0db84a5000-2b0db86a5000 ---p 00005000 fd:00 30968900 /path/to/local/lib/openbabel/2.2.99/featformat.so

2b0db86a5000-2b0db86a6000 rw-p 00005000 fd:00 30968900 /path/to/local/lib/openbabel/2.2.99/featformat.so

2b0db86a6000-2b0db86ba000 r-xp 00000000 fd:00 30968927 /path/to/local/lib/openbabel/2.2.99/chemkinformat.so

2b0db86ba000-2b0db88ba000 ---p 00014000 fd:00 30968927 /path/to/local/lib/openbabel/2.2.99/chemkinformat.so

2b0db88ba000-2b0db88bb000 rw-p 00014000 fd:00 30968927 /path/to/local/lib/openbabel/2.2.99/chemkinformat.so

2b0db88bb000-2b0db88c0000 r-xp 00000000 fd:00 30968879 /path/to/local/lib/openbabel/2.2.99/CSRformat.so

2b0db88c0000-2b0db8abf000 ---p 00005000 fd:00 30968879 /path/to/local/lib/openbabel/2.2.99/CSRformat.so

2b0db8abf000-2b0db8ac0000 rw-p 00004000 fd:00 30968879 /path/to/local/lib/openbabel/2.2.99/CSRformat.so

2b0db8ac0000-2b0db8ad3000 r-xp 00000000 fd:00 30968848 /path/to/local/lib/openbabel/2.2.99/inchiformat.so

2b0db8ad3000-2b0db8cd3000 ---p 00013000 fd:00 30968848 /path/to/local/lib/openbabel/2.2.99/inchiformat.so

2b0db8cd3000-2b0db8cd4000 rw-p 00013000 fd:00 30968848 /path/to/local/lib/openbabel/2.2.99/inchiformat.so

2b0db8cd4000-2b0db8ce3000 r-xp 00000000 fd:00 30968859 /path/to/local/lib/openbabel/2.2.99/adfformat.so

2b0db8ce3000-2b0db8ee3000 ---p 0000f000 fd:00 30968859 /path/to/local/lib/openbabel/2.2.99/adfformat.so

2b0db8ee3000-2b0db8ee4000 rw-p 0000f000 fd:00 30968859 /path/to/local/lib/openbabel/2.2.99/adfformat.so

2b0db8ee4000-2b0db8ee9000 r-xp 00000000 fd:00 30968891 /path/to/local/lib/openbabel/2.2.99/cccformat.so

2b0db8ee9000-2b0db90e8000 ---p 00005000 fd:00 30968891 /path/to/local/lib/openbabel/2.2.99/cccformat.so

2b0db90e8000-2b0db90e9000 rw-p 00004000 fd:00 30968891 /path/to/local/lib/openbabel/2.2.99/cccformat.so

2b0db90e9000-2b0db90ee000 r-xp 00000000 fd:00 30968910 /path/to/local/lib/openbabel/2.2.99/mpqcformat.so

2b0db90ee000-2b0db92ee000 ---p 00005000 fd:00 30968910 /path/to/local/lib/openbabel/2.2.99/mpqcformat.so

2b0db92ee000-2b0db92ef000 rw-p 00005000 fd:00 30968910 /path/to/local/lib/openbabel/2.2.99/mpqcformat.so

2b0db92ef000-2b0db92f4000 r-xp 00000000 fd:00 30968922 /path/to/local/lib/openbabel/2.2.99/xedformat.so

2b0db92f4000-2b0db94f3000 ---p 00005000 fd:00 30968922 /path/to/local/lib/openbabel/2.2.99/xedformat.so

2b0db94f3000-2b0db94f4000 rw-p 00004000 fd:00 30968922 /path/to/local/lib/openbabel/2.2.99/xedformat.so

2b0db94f4000-2b0db94fb000 r-xp 00000000 fd:00 30968866 /path/to/local/lib/openbabel/2.2.99/gulpformat.so

2b0db94fb000-2b0db96fa000 ---p 00007000 fd:00 30968866 /path/to/local/lib/openbabel/2.2.99/gulpformat.so

2b0db96fa000-2b0db96fb000 rw-p 00006000 fd:00 30968866 /path/to/local/lib/openbabel/2.2.99/gulpformat.so

2b0db96fb000-2b0db96ff000 r-xp 00000000 fd:00 30968858 /path/to/local/lib/openbabel/2.2.99/titleformat.so

2b0db96ff000-2b0db98ff000 ---p 00004000 fd:00 30968858 /path/to/local/lib/openbabel/2.2.99/titleformat.so

2b0db98ff000-2b0db9900000 rw-p 00004000 fd:00 30968858 /path/to/local/lib/openbabel/2.2.99/titleformat.so

2b0db9900000-2b0db9906000 r-xp 00000000 fd:00 30968915 /path/to/local/lib/openbabel/2.2.99/pcmodelformat.so

2b0db9906000-2b0db9b06000 ---p 00006000 fd:00 30968915 /path/to/local/lib/openbabel/2.2.99/pcmodelformat.so

2b0db9b06000-2b0db9b07000 rw-p 00006000 fd:00 30968915 /path/to/local/lib/openbabel/2.2.99/pcmodelformat.so

2b0db9b07000-2b0db9b18000 r-xp 00000000 fd:00 30968862 /path/to/local/lib/openbabel/2.2.99/gamessformat.so

2b0db9b18000-2b0db9d18000 ---p 00011000 fd:00 30968862 /path/to/local/lib/openbabel/2.2.99/gamessformat.so

2b0db9d18000-2b0db9d19000 rw-p 00011000 fd:00 30968862 /path/to/local/lib/openbabel/2.2.99/gamessformat.so

2b0db9d19000-2b0db9d1f000 r-xp 00000000 fd:00 30968904 /path/to/local/lib/openbabel/2.2.99/ghemicalformat.so

2b0db9d1f000-2b0db9f1e000 ---p 00006000 fd:00 30968904 /path/to/local/lib/openbabel/2.2.99/ghemicalformat.so

2b0db9f1e000-2b0db9f1f000 rw-p 00005000 fd:00 30968904 /path/to/local/lib/openbabel/2.2.99/ghemicalformat.so

2b0db9f1f000-2b0db9f2b000 r-xp 00000000 fd:00 30968926 /path/to/local/lib/openbabel/2.2.99/chemdrawcdx.so

2b0db9f2b000-2b0dba12b000 ---p 0000c000 fd:00 30968926 /path/to/local/lib/openbabel/2.2.99/chemdrawcdx.so

2b0dba12b000-2b0dba12c000 rw-p 0000c000 fd:00 30968926 /path/to/local/lib/openbabel/2.2.99/chemdrawcdx.so

2b0dba12c000-2b0dba131000 r-xp 00000000 fd:00 30968867 /path/to/local/lib/openbabel/2.2.99/hinformat.so

2b0dba131000-2b0dba331000 ---p 00005000 fd:00 30968867 /path/to/local/lib/openbabel/2.2.99/hinformat.so

2b0dba331000-2b0dba332000 rw-p 00005000 fd:00 30968867 /path/to/local/lib/openbabel/2.2.99/hinformat.so

2b0dba332000-2b0dba337000 r-xp 00000000 fd:00 30968917 /path/to/local/lib/openbabel/2.2.99/shelxformat.so

2b0dba337000-2b0dba537000 ---p 00005000 fd:00 30968917 /path/to/local/lib/openbabel/2.2.99/shelxformat.so

2b0dba537000-2b0dba538000 rw-p 00005000 fd:00 30968917 /path/to/local/lib/openbabel/2.2.99/shelxformat.so

7ffffc6a4000-7ffffc6c5000 rw-p 7ffffc6a4000 00:00 0 [stack]

ffffffffff600000-fffffff Aborted

$ more out.smi n1c(nc2c(c1N(C)C)cccc2)c1c(O)cccc1

Original comment by: makio323

openbabel-bot commented 14 years ago

My apologies - I didn't read your comment the full way down. Reopened!

Original comment by: @baoilleach

openbabel-bot commented 14 years ago

Is this bug still present in 2.3.0rc1?

Original comment by: @ghutchis

serval2412 commented 6 years ago

On pc Debian x86-64 with master sources updated today, I tried to reproduce the original pb. Here what I got: julien@debian:~/projects/openbabel/build/bin$ ./babel ../../bugs/ten.smi -ofs This will prepare an index of ../../bugs/ten.smi and may take some time... It contains 10 molecules It took 0.077262 seconds 6 molecules converted 5 audit log messages julien@debian:~/projects/openbabel/build/bin$ ./babel ../../bugs/ten.fs -ifs-sNc2nc(c1ccccc1)nc3ccccc23' out.smi 1 candidates from fingerprint search phase 1 molecule converted 12 audit log messages ` So I don't reproduce the pb.