From jingyu at algodon.tamu.edu Mon Feb 13 12:30:31 2006 From: jingyu at algodon.tamu.edu (Jing Yu) Date: Tue Feb 14 04:33:48 2006 Subject: [Acedb-soft] What AceDB "Error status = 139" means? Message-ID: Hello, I got error message "Error status = 139" while loading data into acedb. Does anyone know what that means? - The error message never appears when I load each data independently into an empty database, but will appear when load them together or added more data into a database that with large part of data existing. - I've tried ace_4.9f, ace_4.9p, etc.; - The systems so far I've tried are: 1. SunOS baumwolle 5.10 Generic sun4u sparc SUNW,Ultra-4 2. SunOS algodon 5.8 Generic_108528-21 sun4u sparc SUNW,Ultra-60 3. Linux ceres 2.2.16-22smp And they all gave me the same error message. And my dataset is not very large yet, much smaller than that of graingenes (8 block*.wrm files of mine compare to 69 block*.wrm files of graingenes, with the same size of each block*.wrm in /database). Can anyone help me on this? Thank you very much. Jing From jingyu at algodon.tamu.edu Tue Feb 14 09:45:00 2006 From: jingyu at algodon.tamu.edu (Jing Yu) Date: Tue Feb 14 09:50:00 2006 Subject: [Acedb-soft] What AceDB "Error status = 139" means? In-Reply-To: <43F1B936.2090009@imag.fr> Message-ID: > have you tried > loading the data with tace instead of xace? Yes. The error message was given from tace. :( Jing On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote: > hello > > this is a long shot, but just in case it's gtk-related: have you tried > loading the data with tace instead of xace? > > good luck > nicolas > > Jing Yu wrote: > > Hello, > > > > I got error message "Error status = 139" while loading data into > > acedb. Does anyone know what that means? > > > > - The error message never appears when I load each data independently into > > an empty database, but will appear when load them together or added > > more data into a database that with large part of data existing. > > > > - I've tried ace_4.9f, ace_4.9p, etc.; > > - The systems so far I've tried are: > > 1. SunOS baumwolle 5.10 Generic sun4u sparc SUNW,Ultra-4 > > 2. SunOS algodon 5.8 Generic_108528-21 sun4u sparc SUNW,Ultra-60 > > 3. Linux ceres 2.2.16-22smp > > > > And they all gave me the same error message. And my dataset is not very > > large yet, much smaller than that of graingenes (8 block*.wrm files of > > mine compare to 69 block*.wrm files of graingenes, with the same size of > > each block*.wrm in /database). > > > > Can anyone help me on this? Thank you very much. > > > > > > Jing > > > > > > _______________________________________________ > > Acedb mailing list > > Acedb@net.bio.net > > http://www.bio.net/biomail/listinfo/acedb > > -- > ------------------------------------------------------------ > Problems with my digital signature? visit: > http://igc.services.cnrs.fr/Doc/General/trust.html > -------------------- > Nicolas Thierry-Mieg > Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France > tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50 > ------------------------------------------------------------ > From jingyu at algodon.tamu.edu Tue Feb 14 11:21:49 2006 From: jingyu at algodon.tamu.edu (Jing Yu) Date: Tue Feb 14 11:31:56 2006 Subject: [Acedb-soft] What AceDB "Error status = 139" means? In-Reply-To: <43F1F81C.1040002@imag.fr> Message-ID: > alright, how about stack size limits etc...? > if you have very large objects I think this could be a problem That sounds in the right track! I do have very large objects and that's where the problem starts to appear ... I checked the ulimit on my server (see bellow) but not sure what that means? what is the current size that I am having? - Could you give me a hint? By the way, I run tace under bash, shall I try other shell? Thank you. Jing ===================== baumwolle:/usr/bin$ more ulimit #!/bin/ksh -p # #ident "@(#)alias.sh 1.2 00/02/15 SMI" # # Copyright (c) 1995 by Sun Microsystems, Inc. # cmd=`basename $0` $cmd "$@" ===================== On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote: > alright, how about stack size limits etc...? > if you have very large objects I think this could be a problem > > (on bash, the relevant command is ulimit; on csh it's limit) > > > > Jing Yu wrote: > >> have you tried > >>loading the data with tace instead of xace? > > > > > > Yes. The error message was given from tace. :( > > > > Jing > > > > On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote: > > > > > >>hello > >> > >>this is a long shot, but just in case it's gtk-related: have you tried > >>loading the data with tace instead of xace? > >> > >>good luck > >>nicolas > >> > >>Jing Yu wrote: > >> > >>>Hello, > >>> > >>>I got error message "Error status = 139" while loading data into > >>>acedb. Does anyone know what that means? > >>> > >>>- The error message never appears when I load each data independently into > >>>an empty database, but will appear when load them together or added > >>>more data into a database that with large part of data existing. > >>> > >>>- I've tried ace_4.9f, ace_4.9p, etc.; > >>>- The systems so far I've tried are: > >>> 1. SunOS baumwolle 5.10 Generic sun4u sparc SUNW,Ultra-4 > >>> 2. SunOS algodon 5.8 Generic_108528-21 sun4u sparc SUNW,Ultra-60 > >>> 3. Linux ceres 2.2.16-22smp > >>> > >>>And they all gave me the same error message. And my dataset is not very > >>>large yet, much smaller than that of graingenes (8 block*.wrm files of > >>>mine compare to 69 block*.wrm files of graingenes, with the same size of > >>>each block*.wrm in /database). > >>> > >>>Can anyone help me on this? Thank you very much. > >>> > >>> > >>>Jing > >>> > >>> > > -- > ------------------------------------------------------------ > Problems with my digital signature? visit: > http://igc.services.cnrs.fr/Doc/General/trust.html > -------------------- > Nicolas Thierry-Mieg > Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France > tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50 > ------------------------------------------------------------ > From matthews at greengenes.cit.cornell.edu Tue Feb 14 12:04:57 2006 From: matthews at greengenes.cit.cornell.edu (Dave Matthews) Date: Tue Feb 14 12:06:55 2006 Subject: [Acedb-soft] ulimit ["Error status = 139"] Message-ID: <200602141704.k1EH4vD7015135@greengenes.cit.cornell.edu> Hi Jing, > I checked the ulimit on my server > (see bellow) but not sure what that means? what is the current size that > I am having? - Could you give me a hint? In bash, say "ulimit -a". On greengenes this gives me: $ ulimit -a time(seconds) unlimited file(blocks) unlimited data(kbytes) unlimited stack(kbytes) 8192 coredump(blocks) 0 nofiles(descriptors) 64 memory(kbytes) unlimited This reminds me, a few months ago I had to reset the limit on descriptors (the number of files open at the same time) in order to load GrainGenes. User acedb's .cshrc has this: # dem 8nov05: The default 64 descriptors isn't enough for loading ACEDB now. unlimit descriptors This is because GG's database/ directory has so many files, which isn't your problem. If your problem is running out of stack space there might be a message in the system log, /var/adm/messages or wherever it is in baumwolle. - Dave From jingyu at algodon.tamu.edu Tue Feb 14 14:28:03 2006 From: jingyu at algodon.tamu.edu (Jing Yu) Date: Fri Feb 17 03:22:51 2006 Subject: [Acedb-soft] What AceDB "Error status = 139" means? In-Reply-To: <43F20999.3060808@imag.fr> Message-ID: Nicolas, No error appears after setting up ulimit -s unlimited, and everything looks fine. Thank you very much!! Jing On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote: > > bash is fine > > ... > ulimit -a > to see your current limits > > then eg to set the stack size to max, type: > ulimit -s unlimited > > > this will only change the limits for your current shell, hence you > should call tace from it > > when satisfied you can put the correct ulimit commands in your > .bash_profile to make the changes affect every new shell > > > try setting every value to unlimited, at least the memory related ones > (except core, which you can set to 0 since you probably don't read core > dumps anyways) From Nicolas.Thierry-Mieg at imag.fr Thu Feb 16 11:55:49 2006 From: Nicolas.Thierry-Mieg at imag.fr (Nicolas Thierry-Mieg) Date: Fri Feb 17 03:22:54 2006 Subject: [Acedb-soft] acediff bug Message-ID: <43F4AE95.8020006@imag.fr> hi all, I've run into what looks like a bug in acediff. This happens with all versions I've tested, ie today's daily build and the current supported build, both with dynamically linked binaries. I've also tested the current supported static build, same result. All of this, on linux (FC4, kernel 2.6.14-1.1656_FC4 on a pentium4 system) Here is a tiny example to illustrate the problem: $ more wspec/models.wrm ?Interaction Bait UNIQUE ?Text Prey UNIQUE ?Text fns $ more test1.ace Interaction : "test1" Bait "bait1" Prey "prey1" $ more test2.ace Interaction : "test1" Bait "bait1" Prey "prey1" fns $ ace.supported/acediff test1.ace test2.ace reading file 1 - 4 lines read - sorting file 1 reading file 2 - 6 lines read - sorting file 2 performing diff - sorting diff // acediff difference from test1.ace to test2.ace Interaction "test1" Prey "prey1" fns -D Prey "prey1" // end of file As you can see, acediff adds the Prey, then deletes it. After parsing the acediff output, I've obviously lost my Prey info. Funny thing is, if you replace "fns" with "Fns" it's OK... But if you use a different tag you get strange behaviours. eg, using "a_A", acediff also kills the Bait! As far as I can tell (but I haven't tested it much), it works OK when the tag starts with an uppercase letter. Is something wrong with my files or ace binaries?? A+ nicolas -- ------------------------------------------------------------ Nicolas Thierry-Mieg Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50 ------------------------------------------------------------ From Nicolas.Thierry-Mieg at imag.fr Thu Feb 23 10:31:45 2006 From: Nicolas.Thierry-Mieg at imag.fr (Nicolas Thierry-Mieg) Date: Tue Feb 28 04:13:48 2006 Subject: [Acedb-soft] Protein subclass Message-ID: <43FDD561.9050406@imag.fr> hi all, I am trying to define a subclass named Protein, but this doesn't work with any tested xace versions (current supported or daily) Is this forbidden? If yes, shouldn't xace/tace complain when it reads the models? Here is a small example to illustrate: ###################################### $ more models.wrm ?Ligand Protein Sugar ###################################### $ more subclasses.wrm Class Prot Visible Is_a_subclass_of Ligand Filter Protein Class Protein Visible Is_a_subclass_of Ligand Filter Protein Class Sugar Visible Is_a_subclass_of Ligand Filter Sugar ###################################### $ more test.ace Ligand : "lig1" Protein Ligand : "lig2" Sugar ###################################### Initializing the database works fine When parsing test.ace, no errors object lig2 is OK, and shows up in class Sugar but lig1 is NOT in class Protein (ace says that class Protein is empty), although it does show up fine in class Prot. thanks nicolas -- ------------------------------------------------------------ Nicolas Thierry-Mieg Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50 ------------------------------------------------------------ From Nicolas.Thierry-Mieg at imag.fr Fri Feb 24 11:20:04 2006 From: Nicolas.Thierry-Mieg at imag.fr (Nicolas Thierry-Mieg) Date: Tue Feb 28 04:13:51 2006 Subject: [Acedb-soft] acediff bug In-Reply-To: <43F4AE95.8020006@imag.fr> References: <43F4AE95.8020006@imag.fr> Message-ID: <43FF3234.5080309@imag.fr> Skipped content of type multipart/mixed-------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/x-pkcs7-signature Size: 4069 bytes Desc: S/MIME Cryptographic Signature Url : http://www.bio.net/bionet/mm/acedb/attachments/20060224/5a065fd2/smime.bin From mieg at ncbi.nlm.nih.gov Fri Feb 24 12:11:54 2006 From: mieg at ncbi.nlm.nih.gov (Jean Thierry-Mieg) Date: Tue Feb 28 04:13:54 2006 Subject: [Acedb-soft] subscribe Message-ID: <20060224171154.AD33276C17C@mail2.ncbi.nlm.nih.gov> subscribe can i subscribe to that list