From bhagwat@ncbi.nlm.nih.gov Fri Apr 20 15:42:24 2007 Return-Path: Received: from murder (electra.cc.umanitoba.ca [130.179.16.23]) by mbox.cc.umanitoba.ca (Cyrus v2.3.8) with LMTPA; Fri, 20 Apr 2007 15:42:24 -0500 X-Sieve: CMU Sieve 2.3 Received: from electra.cc.umanitoba.ca ([unix socket]) by cc.umanitoba.ca (Cyrus v2.3.8) with LMTPA; Fri, 20 Apr 2007 15:42:24 -0500 X-Sieve: CMU Sieve 2.3 Received: from NIHCESSMTP2.hub.nih.gov (nihcessmtp2.hub.nih.gov [128.231.90.116]) by electra.cc.umanitoba.ca (8.13.0/8.13.0) with ESMTP id l3KKgNS5013211 for ; Fri, 20 Apr 2007 15:42:23 -0500 (CDT) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP2.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Fri, 20 Apr 2007 16:30:22 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Subject: RE: Group: Sequin7.3 segmentation faults on linux Date: Fri, 20 Apr 2007 16:29:30 -0400 Message-ID: In-Reply-To: <1176762600.3103.59.camel@zahn.cc.umanitoba.ca> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Group: Sequin7.3 segmentation faults on linux Thread-Index: AceAdsb9tI/d8aJKTtS6MU35Q3p6HQDEziSQ References: <5C62EAFA82DB944B889B63CCD4B50DD1012B8F9F@NIHCESMLBX8.nih.gov> <1176762600.3103.59.camel@zahn.cc.umanitoba.ca> From: "Bhagwat, Medha \(NIH/NLM/NCBI\) [E]" To: "Brian Fristensky" X-OriginalArrivalTime: 20 Apr 2007 20:30:22.0471 (UTC) FILETIME=[B855E170:01C7838A] X-DCC-UofM-Metrics: electra 1032; Body=1 Fuz1=1 Fuz2=1 Content-Type: text/plain; charset=us-ascii X-Evolution-Source: imap://frist@mail.cc.umanitoba.ca/ Content-Transfer-Encoding: 8bit Dear Brian, I was suggested following solution to try.. Please go to http://rpm.pbone.net/index.php3/stat/3/srodzaj/1/search/libXm.so.2 Next to the 'Fedora4' entry, you will see a link to the 'openmotif' package. Download the file with extension 'rpm' and install this package using the Red Hat package manager (the 'rpm' program) which you should have on your system. Let me know if this helps to solve your problem with Sequin. Best regards, Medha -----Original Message----- From: Brian Fristensky [mailto:frist@cc.umanitoba.ca] Sent: Monday, April 16, 2007 6:30 PM To: Bhagwat, Medha (NIH/NLM/NCBI) [E] Subject: RE: Group: Sequin7.3 segmentation faults on linux On Mon, 2007-04-16 at 15:56, Bhagwat, Medha (NIH/NLM/NCBI) [E] wrote: Here is the ldd output on our Fedora4 system: linux-gate.so.1 => (0x0052f000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x05d24000) libXm.so.2 => /home/psgendb/lib-linux-intel/libXm.so.2 (0x00a3d000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x00885000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x00dea000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x002e4000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x0086e000) libXp.so.6 => /usr/X11R6/lib/libXp.so.6 (0x00c2f000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x00111000) libdl.so.2 => /lib/libdl.so.2 (0x006a0000) libm.so.6 => /lib/libm.so.6 (0x00679000) libc.so.6 => /lib/libc.so.6 (0x0054e000) libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x058ff000) libXft.so.2 => /usr/X11R6/lib/libXft.so.2 (0x00c60000) libXrender.so.1 => /usr/X11R6/lib/libXrender.so.1 (0x001e4000) libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x058d3000) /lib/ld-linux.so.2 (0x00530000) libz.so.1 => /usr/lib/libz.so.1 (0x006a6000) libexpat.so.0 => /usr/lib/libexpat.so.0 (0x008ef000) Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Warning: XtRemoveGrab asked to remove a widget not on the list Segmentation fault You'll notice that libXm.so.2 is not in the system libraries, but had to be added to one of my own directories. I run sequin from a wrapper script that adds /home/psgendb/lib-linux-intel/ to the LD_LIBRARY_PATH. I added a line to the script to run ldd just before launching sequin. The Warning messages may give some clue as to what the problem is. libXm.so.2 is a very old version of this library. It has not been present in Red Hat/Fedora releases since at least Fedora4, and probably earlier than that. It is also not present on recent releases of Gentoo Linux. The only way I have been able to get Sequin to run on Linux for the last few years (at least as far back as Sequin 5.35) has been to keep a copy of libXm.so.2 around. That has not worked very well. It doesn't work to simply make a symbolic link called 'libXm.so.2' that links to libXm.so.3. That results in sequin windows appearing with no text, and a bunch of error messages. It may be the case that sequin needs to be rebuilt using a more recent libXm.so. BF > Dear Colleague, > > After you have installed the Linux version of Sequin from > ftp://ftp.ncbi.nih.gov/sequin/ , please send me the output for ldd > command for the directory that contains Sequin. For example, > > wheeler@quark0:~> ldd /netopt/ncbi_tools/bin/sequin > libXm.so.2 => /usr/X11R6/lib/libXm.so.2 (0x40020000) > libXmu.so.6 => /usr/local/xcompat/lib/libXmu.so.6 (0x40141000) > libXt.so.6 => /usr/local/xcompat/lib/libXt.so.6 (0x40157000) > libX11.so.6 => /usr/local/xcompat/lib/libX11.so.6 (0x401a9000) > libXext.so.6 => /usr/local/xcompat/lib/libXext.so.6 > (0x4029b000) > libm.so.6 => /lib/libm.so.6 (0x402a9000) > libc.so.6 => /lib/libc.so.6 (0x402cb000) > libSM.so.6 => /usr/local/xcompat/lib/libSM.so.6 (0x403fa000) > libICE.so.6 => /usr/local/xcompat/lib/libICE.so.6 (0x40403000) > libXp.so.6 => /usr/X11R6/lib/libXp.so.6 (0x4041b000) > libXau.so.6 => /usr/local/xcompat/lib/libXau.so.6 (0x40424000) > libXdmcp.so.6 => /usr/local/xcompat/lib/libXdmcp.so.6 > (0x40427000) > libdl.so.2 => /lib/libdl.so.2 (0x4042c000) > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) > > I will try to see if you can use Sequin on your computer without > recompiling. > > Best regards, > > Medha Bhagwat, > > > > ------------- Begin Forwarded Message ------------- > > Delivered-To: info@mailgw.ncbi.nlm.nih.gov > X-IronPortListener: CES-Inbound > X-SBRS: 4.7 > X-IronPort-Anti-Spam-Filtered: true > X-IronPort-Anti-Spam-Result: > AgAAAE7rIEaCsxAXk2dsb2JhbACPZCQBAQEBBwgGBwgb > Subject: Sequin7.3 segmentation faults on linux > From: Brian Fristensky > To: info@ncbi.nlm.nih.gov > Mime-Version: 1.0 > Date: Sat, 14 Apr 2007 16:56:11 -0500 > Content-Transfer-Encoding: 7bit > X-OriginalArrivalTime: 14 Apr 2007 21:56:12.0830 (UTC) > FILETIME=[B7B5CBE0:01C77EDF] > > I have previously reported Segmentation fault errors > at many places in Sequin on Linux-Intel, and received > the following reply: > > > > Dear Colleague, > > > > > > There are many distributions of Linux, and they contain different > > versions of libraries. If we statically linked all libraries the size > > of the executable would be very large, and any library bug fixes that > > are later made to a particular version of Linux would not be available > > to the user. > > > > The crash does not occur in testing on Linux at NCBI. It is common > for > > such crashes to occur due to "version skew" when libraries are added > > manually. > > > > The only reasonable solution for Linux users who have problems with > one > > of our applications is to compile it from the source files on his own > > system. That guarantees that he has a consistent set of libraries > that > > work properly together. > > > > > > > > Best regards, > > > > Hanguan Liu > > NCBI User Services > > This problem still exists in Sequin7.3. However, I can't > try recompiling as suggested above because as far as > I can determine, the source code is not available > at the NCBI FTP site. > > I still contend that a statically-linked Linux version > would be far more reliable than asking each Linux > user to recompile. Nonetheless, if source code was > available, with thorough instructions, I would attempt to > try recompiling. Is the source code available? > -- ====================================== Brian Fristensky Department of Plant Science University of Manitoba Winnipeg, MB R3T 2N2 CANADA frist@cc.umanitoba.ca Phone: 204-474-6085 FAX: 204-474-7528 http://home.cc.umanitoba.ca/~frist/ ==================================================== If you really want to understand Science, go to the junk drawer in your kitchen and pull out your tangled collection of string. Carefully work it apart, kneed it with your fingers, pull and untwist, until you have a neat coil. You will need patience, dexterity, perseverence, creativity, the ability to view the problem from all angles, and the ability to learn, as you go, the tricks that help you get all of the knots out. Science starts with an untelligible mess, and refines it into a surprisingly simple model. ====================================================