[Staden] Re: gap4 running problem load_alignment_matrix gap.tcl line 674

Paul Donohue staden at TopQuark.net
Fri Jan 6 10:33:52 EST 2006


I wish I had found this link earlier:
https://sourceforge.net/forum/forum.php?thread_id=1373652&forum_id=347718

On Thu, Jan 05, 2006 at 09:16:31PM -0500, Paul Donohue wrote:
> I've come across this problem a couple times now.  It's quite annoying.
> 
> This error message seems to mean there is a library problem.
> 
> If a library fails to load during initialization, gap4 continues with the rest of the initialization sequence as if nothing went wrong, and only dies when it hits this "load_alignment_matrix" command.  I have no clue why it doesn't detect the library failure immediately and provide a useful error message.
> 
> I'm using Debian Testing, and installing the libg2c0 and libstdc++5 packages seems to be sufficient to make gap4 happy at the moment.
> 
> If you're using another linux distribution, you'll need to figure out which libraries it needs on your own.  The best way I've found to do this is to run:
> 
> strace gap4 > output.txt
> 
> After this finishes, look at the output.txt file and try to figure out which libraries failed to load.
> 
> A successful library load might look something like this:
> open("/usr/local/Staden/lib/linux-binaries/tls/i686/sse2/cmov/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/tls/i686/sse2/cmov", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/tls/i686/sse2/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/tls/i686/sse2", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/tls/i686/cmov/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/tls/i686/cmov", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/tls/i686/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/tls/i686", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/tls/sse2/cmov/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/tls/sse2/cmov", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/tls/sse2/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/tls/sse2", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/tls/cmov/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/tls/cmov", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/tls/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/tls", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/i686/sse2/cmov/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/i686/sse2/cmov", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/i686/sse2/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/i686/sse2", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/i686/cmov/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/i686/cmov", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/i686/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/i686", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/sse2/cmov/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/sse2/cmov", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/sse2/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/sse2", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/cmov/libncurses.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/local/Staden/lib/linux-binaries/cmov", 0xbfec6da4) = -1 ENOENT (No such file or directory)
> open("/usr/local/Staden/lib/linux-binaries/libncurses.so.5", O_RDONLY) = 3
> read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0p\343\0"..., 512) = 512
> fstat64(3, {st_mode=S_IFREG|0644, st_size=268396, ...}) = 0
> old_mmap(NULL, 273580, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0
> xb7f6f000
> old_mmap(0xb7fa9000, 36864, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENY
> WRITE, 3, 0x39000) = 0xb7fa9000
> close(3)                                = 0
> 
> (Note that it tried to find the library in a whole bunch of directories, but it eventually found a copy and successfully opened and read it)
> 
> A failed library might look something like this:
> open("/usr/local/Staden/lib/linux-binaries/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
> open("/lib/tls/i686/sse2/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/tls/i686/sse2/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/lib/tls/i686/sse2/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/tls/i686/sse2", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/lib/tls/i686/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/tls/i686/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/lib/tls/i686/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/tls/i686", 0xbfbf2e38)     = -1 ENOENT (No such file or directory)
> open("/lib/tls/sse2/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/tls/sse2/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/lib/tls/sse2/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/tls/sse2", 0xbfbf2e38)     = -1 ENOENT (No such file or directory)
> open("/lib/tls/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/tls/cmov", 0xbfbf2e38)     = -1 ENOENT (No such file or directory)
> open("/lib/tls/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/tls", {st_mode=S_IFDIR|0755, st_size=1560, ...}) = 0
> open("/lib/i686/sse2/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/i686/sse2/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/lib/i686/sse2/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/i686/sse2", 0xbfbf2e38)    = -1 ENOENT (No such file or directory)
> open("/lib/i686/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/i686/cmov", 0xbfbf2e38)    = -1 ENOENT (No such file or directory)
> open("/lib/i686/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/i686", 0xbfbf2e38)         = -1 ENOENT (No such file or directory)
> open("/lib/sse2/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/sse2/cmov", 0xbfbf2e38)    = -1 ENOENT (No such file or directory)
> open("/lib/sse2/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/sse2", 0xbfbf2e38)         = -1 ENOENT (No such file or directory)
> open("/lib/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/lib/cmov", 0xbfbf2e38)         = -1 ENOENT (No such file or directory)
> open("/lib/libstdc++.so.5", O_RDONLY)   = -1 ENOENT (No such file or directory)
> stat64("/lib", {st_mode=S_IFDIR|0755, st_size=3976, ...}) = 0
> open("/usr/lib/tls/i686/sse2/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/tls/i686/sse2/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/tls/i686/sse2/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/tls/i686/sse2", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/tls/i686/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/tls/i686/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/tls/i686/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/tls/i686", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/tls/sse2/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/tls/sse2/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/tls/sse2/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/tls/sse2", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/tls/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/tls/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/tls/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/tls", {st_mode=S_IFDIR|0755, st_size=136, ...}) = 0
> open("/usr/lib/i686/sse2/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/i686/sse2/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/i686/sse2/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/i686/sse2", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/i686/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/i686/cmov", {st_mode=S_IFDIR|0755, st_size=192, ...}) = 0
> open("/usr/lib/i686/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/i686", {st_mode=S_IFDIR|0755, st_size=72, ...}) = 0
> open("/usr/lib/sse2/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/sse2/cmov", 0xbfbf2e38) = -1 ENOENT (No such file or directory)
> open("/usr/lib/sse2/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/sse2", 0xbfbf2e38)     = -1 ENOENT (No such file or directory)
> open("/usr/lib/cmov/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib/cmov", 0xbfbf2e38)     = -1 ENOENT (No such file or directory)
> open("/usr/lib/libstdc++.so.5", O_RDONLY) = -1 ENOENT (No such file or directory)
> stat64("/usr/lib", {st_mode=S_IFDIR|0755, st_size=37168, ...}) = 0
> munmap(0xb7b08000, 43978)               = 0
> munmap(0xb7b13000, 17508)               = 0
> munmap(0xb7871000, 2353440)             = 0
> munmap(0xb7ab0000, 196960)              = 0
> munmap(0xb7849000, 163396)              = 0
> munmap(0xb7aff000, 34708)               = 0
> munmap(0xb7822000, 158368)              = 0
> munmap(0xb7806000, 114596)              = 0
> 
> 
> (Note that it tried to find the library in a whole bunch of directories again, but this time it never actually found a copy.  And after the block of open/stat64 commands, you see a series of memory deallocation commands, instead of the file read/memory allocation/file close commands seen earlier.)
> 
> Install whatever files gap4 is failing to load, and hopefully your problems will go away.
> 
> -Paul
> 
> >Thu Aug 4 04:26:31 EST 2005
> >
> >Hi,
> >
> >I am beginner in using staden and first I fall in to problems with
> >installing/running it.
> >All staden folders are copied in /usr/local/bin/staden
> >and following lines are added to .bashrc
> >STADENROOT=/usr/local/bin/staden; export STADENROOT
> >source $STADENROOT/staden.profile
> >
> >But when I running gap4 I got followin error
> >
> >[tmargus at localhost ~]$ gap4
> >invalid command name "load_alignment_matrix"
> >    while executing
> >"load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
> >    (file "/usr/local/bin/staden/lib/gap/gap.tcl" line 674)
> >
> >
> >Any help and suggestions are welcome
> >
> > Tõnu Margus
> >
> >Tartu university
> >Riia 23
> >Tartu 51010
> >Estonia
> 



More information about the Staden mailing list