[Bioclusters] Opteron Perl64 segfault issues
Joseph Landman
bioclusters@bioinformatics.org
16 Aug 2003 12:22:55 -0400
Hi Nathan:
(punchline: the newly compiled SUSE m64 binaries seem to work)
Using the version I just put up at my site, and using the -n switch on
the formatdb gives me this for the blastall run:
BLASTX 2.2.6 [Apr-09-2003]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.
Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 25094 Lambda-PRL2 Arabidopsis thaliana cDNA clone 251F2T7, mRNA
sequence.
(604 letters)
Database: nr
1,479,768 sequences; 476,959,297 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits)
Value
gb|AAK91384.1| AT3g19760/MMB12_21 [Arabidopsis thaliana] >gi|250...
184 1e-45
ref|NP_188610.1| eukaryotic translation initiation factor 4A (eI...
184 1e-45
pir||T51737 RNA helicase RH2 [imported] - Arabidopsis thaliana >...
184 1e-45
ref|XP_312776.1| ENSANGP00000020417 [Anopheles gambiae] >gi|3017...
178 6e-44
.
.
.
>gb|AAK91384.1| AT3g19760/MMB12_21 [Arabidopsis thaliana]
gb|AAN72219.1| At3g19760/MMB12_21 [Arabidopsis thaliana]
Length = 408
Score = 184 bits (466), Expect = 1e-45
Identities = 91/91 (100%), Positives = 91/91 (100%)
Frame = +3
Query: 27 NEFRSGDSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINF
206
NEFRSGDSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINF
Sbjct: 318 NEFRSGDSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINF
377
Query: 207 VKSDDIKILRDIEQYYSTQIDEMPMNVADLI 299
VKSDDIKILRDIEQYYSTQIDEMPMNVADLI
Sbjct: 378 VKSDDIKILRDIEQYYSTQIDEMPMNVADLI 408
>ref|NP_188610.1| eukaryotic translation initiation factor 4A (eIF-4A),
putative
[Arabidopsis thaliana]
Length = 408
Score = 184 bits (466), Expect = 1e-45
.
.
.
In short, it appears to work, though I need to compare this to the same
run I have done by hand a while ago. If you want my test cases (and
scripts), send me an email offline, and I will give you a pointer to
them.
Joe
On Sat, 2003-08-16 at 11:38, Nathan O. Siemers wrote:
>
> Nope. I feared this would not solve the corruption of the blast
> database itself:
>
> (testy database created with formatdb -n testy...)
>
> this is with my compiled version of formatdb using the suggested IBM
> config mod...
>
>
>
> opt:/u1/gcgblast # blastall -v 1 -b 1 -a 2 -d testy -i refseq_fly_prot
> -p tblastn
> TBLASTN 2.2.6 [Apr-09-2003]
>
>
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs", Nucleic Acids Res. 25:3389-3402.
>
> Query= BMSPROT:NP_478140 histone H2A; histone [Drosophila
> melanogaster]. [Subset=EMBL/GENBANK/DDBJ,REFSEQ]
> (124 letters)
>
> Database: test
> 62,463 sequences; 6,244,139,235 total letters
>
> Searching..................................................done
>
> Score E
> Sequences producing significant alignments: (bits)
> Value
>
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
> Unknown
> 199 5e-50
>
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
>
> Score = 199 bits (506), Expect = 5e-50
>
> Query: 16 SRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 75
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
>
> Query: 76 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 121
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
>
>
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
>
> Score = 196 bits (497), Expect = 5e-49
> Identities = 0/106 (0%), Positives = 0/106 (0%)
> Frame = +2
>
> Query: 16 SRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 75
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
>
> Query: 76 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 121
> [blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> pointer [0] type [1] not found
>
>
>
>
> Joseph Landman wrote:
> > Hi Nathan, Carlos, et al:
> >
> > I have verified on the test system that a formatdb without the -n
> > option gives you the (null).[pn]al. Using the -n option provides a
> > workaround. That is
> >
> > formatdb -i swissprot -v 2 -o T -p T
> >
> > does not work properly, though
> >
> > formatdb -i swissprot -n swissprot -v 2 -o T -p T
> >
> > does. I have not had the chance to try a real run, I will do that a
> > little later today.
> >
> > This formatdb is
> >
> > file formatdb
> > formatdb: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV),
> > dynamically linked (uses shared libs), not stripped
> >
> > I rebuilt (as an m64 binary!) using Lawrence's recommended define, and
> > ran that as well:
> >
> > test> file formatdb
> > formatdb: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV),
> > dynamically linked (uses shared libs), not stripped
> > test> formatdb -i swissprot -n swissprot -v 2 -o T -p T
> > test> ls
> > formatdb.log swissprot.06.pin swissprot.12.psd swissprot.19.phr
> > swissprot swissprot.06.pnd swissprot.12.psi swissprot.19.pin
> > swissprot.00.phr swissprot.06.pni swissprot.12.psq swissprot.19.pnd
> > swissprot.00.pin swissprot.06.psd swissprot.13.phr swissprot.19.pni
> > swissprot.00.pnd swissprot.06.psi swissprot.13.pin swissprot.19.psd
> > swissprot.00.pni swissprot.06.psq swissprot.13.pnd swissprot.19.psi
> > swissprot.00.psd swissprot.07.phr swissprot.13.pni swissprot.19.psq
> > swissprot.00.psi swissprot.07.pin swissprot.13.psd swissprot.20.phr
> > swissprot.00.psq swissprot.07.pnd swissprot.13.psi swissprot.20.pin
> > swissprot.01.phr swissprot.07.pni swissprot.13.psq swissprot.20.pnd
> > swissprot.01.pin swissprot.07.psd swissprot.14.phr swissprot.20.pni
> > swissprot.01.pnd swissprot.07.psi swissprot.14.pin swissprot.20.psd
> > swissprot.01.pni swissprot.07.psq swissprot.14.pnd swissprot.20.psi
> > swissprot.01.psd swissprot.08.phr swissprot.14.pni swissprot.20.psq
> > swissprot.01.psi swissprot.08.pin swissprot.14.psd swissprot.21.phr
> > swissprot.01.psq swissprot.08.pnd swissprot.14.psi swissprot.21.pin
> > swissprot.02.phr swissprot.08.pni swissprot.14.psq swissprot.21.pnd
> > swissprot.02.pin swissprot.08.psd swissprot.15.phr swissprot.21.pni
> > swissprot.02.pnd swissprot.08.psi swissprot.15.pin swissprot.21.psd
> > swissprot.02.pni swissprot.08.psq swissprot.15.pnd swissprot.21.psi
> > swissprot.02.psd swissprot.09.phr swissprot.15.pni swissprot.21.psq
> > swissprot.02.psi swissprot.09.pin swissprot.15.psd swissprot.22.phr
> > swissprot.02.psq swissprot.09.pnd swissprot.15.psi swissprot.22.pin
> > swissprot.03.phr swissprot.09.pni swissprot.15.psq swissprot.22.pnd
> > swissprot.03.pin swissprot.09.psd swissprot.16.phr swissprot.22.pni
> > swissprot.03.pnd swissprot.09.psi swissprot.16.pin swissprot.22.psd
> > swissprot.03.pni swissprot.09.psq swissprot.16.pnd swissprot.22.psi
> > swissprot.03.psd swissprot.10.phr swissprot.16.pni swissprot.22.psq
> > swissprot.03.psi swissprot.10.pin swissprot.16.psd swissprot.23.phr
> > swissprot.03.psq swissprot.10.pnd swissprot.16.psi swissprot.23.pin
> > swissprot.04.phr swissprot.10.pni swissprot.16.psq swissprot.23.pnd
> > swissprot.04.pin swissprot.10.psd swissprot.17.phr swissprot.23.pni
> > swissprot.04.pnd swissprot.10.psi swissprot.17.pin swissprot.23.psd
> > swissprot.04.pni swissprot.10.psq swissprot.17.pnd swissprot.23.psi
> > swissprot.04.psd swissprot.11.phr swissprot.17.pni swissprot.23.psq
> > swissprot.04.psi swissprot.11.pin swissprot.17.psd swissprot.24.phr
> > swissprot.04.psq swissprot.11.pnd swissprot.17.psi swissprot.24.pin
> > swissprot.05.phr swissprot.11.pni swissprot.17.psq swissprot.24.pnd
> > swissprot.05.pin swissprot.11.psd swissprot.18.phr swissprot.24.pni
> > swissprot.05.pnd swissprot.11.psi swissprot.18.pin swissprot.24.psd
> > swissprot.05.pni swissprot.11.psq swissprot.18.pnd swissprot.24.psi
> > swissprot.05.psd swissprot.12.phr swissprot.18.pni swissprot.24.psq
> > swissprot.05.psi swissprot.12.pin swissprot.18.psd swissprot.pal
> > swissprot.05.psq swissprot.12.pnd swissprot.18.psi
> > swissprot.06.phr swissprot.12.pni swissprot.18.psq
> > test> cat swissprot.pal
> > #
> > # Alias file created Sat Aug 16 16:03:34 2003
> > #
> > #
> > TITLE swissprot
> > #
> > DBLIST swissprot.00 swissprot.01 swissprot.02 swissprot.03 swissprot.04
> > swissprot.05 swissprot.06 swissprot.07 swissprot.08 swissprot.09
> > swissprot.10 swissprot.11 swissprot.12 swissprot.13 swissprot.14
> > swissprot.15 swissprot.16 swissprot.17 swissprot.18 swissprot.19
> > swissprot.20 swissprot.21 swissprot.22 swissprot.23 swissprot.24
> > #
> > #GILIST
> > #
> > #OIDLIST
> > #
> >
> > Looks like this is working. Is the use of the -n switch on formatdb an
> > acceptable workaround for the (null) problem?
> >
> > Note: This machine doesn't have enough disk space to test the binaries
> > with a big database file. I will post the SUSE 8.2 compiled binaries
> > and linux.ncbi.mk in a bit. Please let me know if they work for you.
> > They will be in http://scalableinformatics.com/downloads/opteron/ncbi as
> > blastall.suse.gz and formatdb.suse.gz as well as the
> > ncbitoolkit.suse.tar.gz tarball.
> >
> > Note: I have reorganized the opteron compiled bits to reside under
> > opteron/...
> >
> > Joe
> >
> >
> > On Sat, 2003-08-16 at 07:37, Nathan Siemers wrote:
> >
> >>Hello Joe,
> >>
> >>Folks at IBM are suggesting this mod to compile blastall on opteron 64,
> >>and for the blastall binary itself it
> >>seems to work: If the full 64 bit works on redhat, then updating the
> >>gcc and libs may be the easiest way
> >>to go, but I would appreciate it if you test formatdb on large (6gig)
> >>input databases to see what it does...
> >>see the notes below.
> >>
> >>
> >>Nathan
> >>
> >>
> >>
> >>2) BLAST
> >>Dr. Lawrence Hannon successfully resolved the coredump problem that he
> >>encountered with the 64-bit BLAST built using the default configuration
> >>files with gcc as downloaded from NCBI. He modified the NCBI_CFLAGS1 flag
> >>in ncbi/platform/linux.ncbi.mk to include the definition flag
> >>-DOS_UNIX_PPCLINUX which effects how the source ncbi/build/tsprintf.c
> >>treats variable arguments to get the gcc build to work. Both Lawrence
> >>and I had tested this 64-bit BLAST and so far all tests were successful.
> >>
> >>
> >>However, the resulting binaries haven't passed all my tests. In
> >>particular, formatdb
> >>seems to have problems creating intact dbs when it creates multiple volumes:
> >>
> >>Tests against small databases seem to be working, but...
> >>
> >> Some things are still not functioning perfectly:
> >>
> >> Given a large database file that must be split up into volumes, the
> >>resulting .nal or .pal file produced by formatdb does not have the name
> >>of the original file, a '(null)' is produced instead:
> >>
> >>-rw-r--r-- 1 rioscb root 270 Aug 15 08:25 (null).nal
> >>
> >> This was run via:
> >>
> >> formatdb -p F -i file
> >>
> >> where file was a 6gig database of nucleotide sequences.
> >>
> >>The file contents of the .nal file also has (null) where the original
> >>file name is supposed to be:
> >>
> >>#
> >># Alias file created Fri Aug 15 08:25:05 2003
> >>#
> >>#
> >>TITLE NCBI_31_Masked_Chromosomes.shredded.100000.50000
> >>#
> >>DBLIST (null).00 (null).01 (null).02 (null).03 (null).04 (null).05
> >>(null).06 (null).07 (null).08 (null).09 (null).10 (null).11 (null).12
> >>#
> >>#GILIST
> >>#
> >>#OIDLIST
> >>#
> >>
> >>Manually fixing this .nal file and renaming it appropriately lets me run
> >>blastall against the file, but there are severe errors: possible pointer
> >>problems, blastall can't retrieve the name of the query, and the
> >>alignment is garbage:
> >>
> >>________________________
> >># blastall -a 2 -p tblastn -v 1 -b 1 -e 0.00001 -i refseq_fly_prot -d
> >>NCBI_31_Masked_Chromosomes.shredded.100000.50000
> >>__________________________
> >>
> >>
> >>TBLASTN 2.2.6 [Apr-09-2003]
> >>
> >>
> >>Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
> >>Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> >>"Gapped BLAST and PSI-BLAST: a new generation of protein database search
> >>programs", Nucleic Acids Res. 25:3389-3402.
> >>
> >>Query= BMSPROT:NP_478140 histone H2A; histone [Drosophila
> >>melanogaster]. [Subset=EMBL/GENBANK/DDBJ,REFSEQ]
> >> (124 letters)
> >>
> >>Database: NCBI_31_Masked_Chromosomes.shredded.100000.50000
> >> 62,463 sequences; 6,244,139,235 total letters
> >>
> >>Searching..................................................done
> >>
> >> Score E
> >>Sequences producing significant alignments: (bits)
> >>Value
> >>
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>Unknown 199 5e-50
> >>
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>
> >> Score = 199 bits (506), Expect = 5e-50
> >>
> >>Query: 16 SRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 75
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>
> >>Query: 76 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 121
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>
> >>
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>
> >> Score = 196 bits (497), Expect = 5e-49
> >> Identities = 0/106 (0%), Positives = 0/106 (0%)
> >> Frame = +2
> >>
> >>Query: 16 SRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 75
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>
> >>Query: 76 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 121
> >>[blastall] ERROR: ncbiapi [000.000] BMSPROT:NP_478140: ObjMgrChoice:
> >>pointer [0] type [1] not found
> >>
> >>
> >>
> >>All this work was done with:
> >>
> >>gcc version:
> >>
> >>Reading specs from /usr/lib64/gcc-lib/x86_64-suse-linux/3.2.2/specs
> >>Configured with: ../configure --enable-threads=posix --prefix=/usr
> >>--with-local-prefix=/usr/local --infodir=/usr/share/info
> >>--mandir=/usr/share/man --libdir=/usr/lib64
> >>--enable-languages=c,c++,f77,objc,java,ada --enable-libgcj
> >>--with-gxx-include-dir=/usr/include/g++ --with-slibdir=/lib
> >>--with-system-zlib --enable-shared --enable-__cxa_atexit x86_64-suse-linux
> >>Thread model: posix
> >>gcc version 3.2.2 (SuSE Linux)
> >>
> >>
> >>ldd on the executables gives:
> >>
> >>opt:/u1/gcgblast # ldd /usr/local/bin/blastall
> >> libm.so.6 => /lib64/libm.so.6 (0x0000002a9566a000)
> >> libpthread.so.0 => /lib64/libpthread.so.0 (0x0000002a957c2000)
> >> libc.so.6 => /lib64/libc.so.6 (0x0000002a958e2000)
> >> /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2
> >>(0x0000002a95556000)
> >>
> >>
> >>
> >>Looking back at the log of the Make, these messages are disturbing, and
> >>they appear throughout the make process:
> >>
> >>gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -O2 -c
> >>-DOS_UNIX_PPCLINUX -I../include -I/usr/X11R6/include -L/usr/X11R6/lib
> >>-DWIN_MOTIF cdnewlib.c
> >>In file included from ../include/ncbi.h:57,
> >> from ../include/asn.h:125,
> >> from ../include/objacces.h:64,
> >> from ../include/cdromlib.h:71,
> >> from cdnewlib.c:208:
> >>../include/ncbilcl.h:104:2: warning: #warning Unknown processor type.
> >>Please define something appropriate.
> >>cdnewlib.c: In function `cd3_CdDocAsnOpen':
> >>cdnewlib.c:1342: warning: cast to pointer from integer of different size
> >>cdnewlib.c: In function `UidIndex_ReadPage':
> >>cdnewlib.c:1937: warning: cast to pointer from integer of different size
> >>cdnewlib.c:1945: warning: cast to pointer from integer of different size
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>Joseph Landman wrote:
> >>
> >>
> >>>Hi Nathan:
> >>>
> >>> I just ran into this myself. I built the binaries on RedHat GinGin64
> >>>with the gcc-3.3 compiler. I just tried a SUSE 8.2 platform, and had to
> >>>recompile the toolkit. If you want to use the binary, I think you need
> >>>the relevant gcc tree installed. I think I might have that here. I
> >>>will look.
> >>>
> >>> For reasons that are not all that clear to me now, I had to use the
> >>>-m32 flag to generate a working binary on SUSE. The -m32 forces the use
> >>>of the IA32 ABI, which means that you cannot use some of the nicer
> >>>features of the Opteron (large memory, 64 bit mode, etc). I hope to
> >>>investigate this more.
> >>>
> >>> A kind soul just gave me access to their opteron for some testing.
> >>>Compiling with -m64 generates a binary, though upon completion of a test
> >>>run, it generates an ABORT. Strace wasn't all that helpful here. I am
> >>>trying to track this down.
> >>>
> >>> I can give you my -m32 binaries if you would like. I would like to
> >>>get the -m64 binaries working (for SUSE).
> >>>
> >>>Joe
> >>>
> >>>On Fri, 2003-08-15 at 22:58, Nathan Siemers wrote:
> >>>
> >>>
> >>>
> >>>>Hello Joe,
> >>>>
> >>>>My default SUSE opteron configuration may not have the libs to run your
> >>>>build:
> >>>>
> >>>>
> >>>>opt:/u1/gcgblast # formatdb -p F -i test &
> >>>>formatdb: /lib64/libc.so.6: version `GLIBC_2.3' not found (required by
> >>>>formatdb)
> >>>>[1] 10941
> >>>>[1] Exit 1 formatdb -p F -i test
> >>>>opt:/u1/gcgblast # ldd /usr/local/bin/formatdb
> >>>>/usr/local/bin/formatdb: /lib64/libc.so.6: version `GLIBC_2.3' not found
> >>>>(required by /usr/local/bin/formatdb)
> >>>> libm.so.6 => /lib64/libm.so.6 (0x0000002a9566a000)
> >>>> libc.so.6 => /lib64/libc.so.6 (0x0000002a957c2000)
> >>>> /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2
> >>>>(0x0000002a95556000)
> >>>>
> >>>>
> >>>>I assume these are 64 bit executables? Is there a newer libc needed?
> >>>>
> >>>>Thanks for your (past and present) help with the opteron platform.
> >>>>
> >>>> Nathan
> >>>>
> >>>>
> >>>>
> >>>>Joseph Landman wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>Hi Doug:
> >>>>>
> >>>>>These are 2.2.6. The tree's VERSION (ncbi/VERSION) reads:
> >>>>>
> >>>>>[landman@squash.scalableinformatics.com:/big/t/ncbi]
> >>>>>8 >cat VERSION
> >>>>>Tue Apr 22 10:41:40 EDT 2003
> >>>>>
> >>>>>Please let me know if you have problems with them. This was a first
> >>>>>pass at getting working systems.
> >>>>>
> >>>>>Joe
> >>>>>
> >>>>>On Tue, 2003-08-12 at 20:17, Doug Shubert wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>>Hello Joe,
> >>>>>>What version of ncbitools are you working with ?
> >>>>>>Doug
> >>>>>>
> >>>>>>Joe Landman wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>Its up. Please let me know if it works. This is a snapshot from a
> >>>>>>>build done in June, Download is
> >>>>>>>http://scalableinformatics.com/downloads/opteron.ncbitools.tar.gz . It
> >>>>>>>is 29MB.
> >>>>>>>
> >>>>>>>Joe
> >>>>>>>
> >>>>>>>On Tue, 2003-08-12 at 15:46, Joe Landman wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>>On Tue, 2003-08-12 at 13:11, Nathan Siemers wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>That's great news, Joe. Has this build passed any regression tests,
> >>>>>>>>>i.e. rigorous
> >>>>>>>>>comparison to output from blastall on other architectures?
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>I have not had an opteron to run on long enough to run my normal tests.
> >>>>>>>>It did generate the same results for my short tests.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>--
> >>>>>>>Joseph Landman, Ph.D
> >>>>>>>Scalable Informatics LLC,
> >>>>>>>email: landman@scalableinformatics.com
> >>>>>>>web : http://scalableinformatics.com
> >>>>>>>phone: +1 734 612 4615
> >>>>>>>
> >>>>>>>_______________________________________________
> >>>>>>>Bioclusters maillist - Bioclusters@bioinformatics.org
> >>>>>>>https://bioinformatics.org/mailman/listinfo/bioclusters
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>_______________________________________________
> >>>>>>Bioclusters maillist - Bioclusters@bioinformatics.org
> >>>>>>https://bioinformatics.org/mailman/listinfo/bioclusters
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>
> >>>>_______________________________________________
> >>>>Bioclusters maillist - Bioclusters@bioinformatics.org
> >>>>https://bioinformatics.org/mailman/listinfo/bioclusters
> >>>>
> >>>>
> >>
> >>_______________________________________________
> >>Bioclusters maillist - Bioclusters@bioinformatics.org
> >>https://bioinformatics.org/mailman/listinfo/bioclusters
--
Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
web: http://scalableinformatics.com
phone: +1 734 612 4615