Hi, Jeff! I was unable to reproduce the problem.
I used the same version of the source http://users.soe.ucsc.edu/~kent/src/blatSrc34.zip and compiled it and ran it. It took 4 minutes for gfServer to finish counting tiles for hg19.2bit and say it was ready. --- gfServer start localhost 18000 -stepSize=5 /gbdb/hg19/hg19.2bit starting untranslated server... Counting tiles in /gbdb/hg19/hg19.2bit Done adding Server ready for queries! --- Here are some things you might think about: Is port 18000 available? Maybe it is already occupied? To see if an old copy of gfServer is still running you can try ps aux | grep gfServer | grep -v grep Is that port blocked by a firewall? Does it work if you wait longer? Does it work if you try it without -stepSize=5, since that would use just half the amount of ram. What does uname -a show? What does this show? file `which gfServer` for me it outputs: /somepath/gfServer: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, stripped -Galt 8/19/2010 7:32 AM, [email protected]: > Hi Galt. > > Sorry for the delay. Here's a little more information: > I'm running on Fedora 11 64-bit. > I compiled gfServer (et al.) from source downloaded from the website: > http://users.soe.ucsc.edu/~kent/src/ . I'm using version 3.4. > > The error when compiling was in jkOwnLib/fuzzyFind.c. Here's the console > output: >> make > ... > ... > ... > K_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc > -I../../../../../inc -o fuzzyFind.o -c fuzzyFind.c > cc1: warnings being treated as errors > fuzzyFind.c: In function ‘lumpHits’: > fuzzyFind.c:1049: error: ‘proto.score’ may be used uninitialized in this > function > make[1]: *** [fuzzyFind.o] Error 1 > make[1]: Leaving directory `/home/jeffreya/Desktop/blat/jkOwnLib' > make: *** [all] Error 2 > > When I removed the -Werror switches (two in that file), everything > compiled without an error. > > Thanks for taking a look at this. > > Jeff > > >> Hi, Jeff! >> >> Where did you get the source code? >> I'd like to know what exactly what version you are using. >> >> Also, what error message did you get before >> removing the -Werror. >> >> We run gfServer on 64-bit CentOS 5.5. >> >> -Galt >> >> On 08/13/10 12:24, [email protected] wrote: >>> I've been experimenting with gfServer on a few different platforms >>> (Windows, Mandriva, etc.) and just ran into my first problem. >>> >>> I've been able to compile and execute the gfServer on both of the >>> previous >>> platforms, but I'm currently trying to run it on Fedora 11 x64 and am >>> having some problems. I start the server with the same files I've used >>> elsewhere (which have worked on other platforms), but it now just stops >>> at >>> "Counting tiles in ..." and never progresses. The index is usually built >>> within 15 minutes on comparable platforms; it's sat for over an hour now >>> without getting past "counting tiles." >>> >>> It consumes RAM the same way as it previously did (~2.2GB for hg19), and >>> it consistently consumes one core of the CPU the whole time. >>> >>>> gfServer start localhost 18000 -stepSize=5 /<directory>/hg19.2bit >>> >>> The only deviation I took from the standard "make" install was the >>> removal >>> of -Werror switches in one make file to get rid of an error as >>> recommended >>> at http://www.mail-archive.com/[email protected]/msg01674.html . >>> >>> Any help is appreciated. >>> >>> Jeff >>> >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
