Folding Forum

by **Spongebob25** » Mon Jan 18, 2010 12:54 am

I upgraded to Ubuntu 10.04 Alpha 2 and now I get an error when trying to run the f@h client.

Code: Select all: # Linux SMP Console Edition ################################################### ############################################################################### Folding@Home Client Version 6.24R3 http://folding.stanford.edu ############################################################################### ############################################################################### Launch directory: /home/spongeboblx/f@h Executable: ./fah6 Arguments: -smp 8 -bigadv -verbosity 9 [23:42:00] - Ask before connecting: No [23:42:00] - User name: Spongebob25 (Team 80856) [23:42:00] - User ID: [23:42:00] - Machine ID: 1 [23:42:00] [23:42:00] Loaded queue successfully. [23:42:00] - Preparing to get new work unit... [23:42:00] - Autosending finished units... [January 17 23:42:00 UTC] [23:42:00] Cleaning up work directory [23:42:00] Trying to send all finished work units [23:42:00] + No unsent completed units remaining. [23:42:00] - Autosend completed [23:42:00] + Attempting to get work packet [23:42:00] - Will indicate memory of 1977 MB [23:42:00] - Connecting to assignment server [23:42:00] Connecting to http://assign.stanford.edu:8080/ fah6: relocation error: /lib/libnss_files.so.2: symbol __rawmemchr, version GLIBC_2.2.5 not defined in file libc.so.6 with link time reference spongeboblx@ubuntu:~/f@h$

by **ChelseaOilman** » Mon Jan 18, 2010 1:03 am

Your not the first to have issues with Ubuntu 10.04.

viewtopic.php?f=55&t=12824

Did you tell the Ubuntu developers there's an issue with 10.04 and F@H?

by **Spongebob25** » Wed Jan 20, 2010 6:40 am

Nope. Don't know where to go to get help.

Here is the error so you don't have to read the log.

fah6: relocation error: /lib/libnss_files.so.2: symbol __rawmemchr, version GLIBC_2.2.5 not defined in file libc.so.6 with link time reference

by **ChelseaOilman** » Wed Jan 20, 2010 7:15 am

Spongebob25 wrote:Nope. Don't know where to go to get help.

http://www.ubuntu.com/community/ReportProblem

by **djchandler** » Fri Jan 22, 2010 9:37 am

Spongebob25 wrote:Nope. Don't know where to go to get help.

Do you have this set up as a chron job, or perhaps installed through an Ubuntu specific script like Origami? Otherwise, I've not heard before that F@H calls libraries from the host system. I've always assumed the F@H client, mpiexec and cores were all self contained and only called each others' sub-routines.

Hopefully you have a Launchpad account since you are beta testing. Your problem with 10.04 needs to be reported at:

https://launchpad.net/ubuntu

There are a couple of places to go for help with Ubuntu as relates to F@H. Perhaps you could inquire through these channels as well.

Team Ubuntu's IRC channel: #ubuntu-folding on FreeNode

Launchpad Team Page: https://launchpad.net/~folding-at-home

Mailing List:- Only available to members of the folding-at-home group on Launchpad. Join the group, and subscribe to the mailing list there.
Address: folding-at-home@lists.launchpad.net
Archives: https://lists.launchpad.net/folding-at-home/

by **linuxfah** » Fri Jan 22, 2010 8:10 pm

The relocation error has to do with the glibc 2.11.1 build that Ubuntu 10.04 comes with. I built 2.11.1 for my Slackware64 systems and have not had any issues folding with this version libc. I also was able to get my glibc build to install on Ubuntu 10.04 Alpha 2 and the folding client works without issues now.

by **error10** » Sat Jan 30, 2010 4:52 am

This post has a workaround which got things working for me.

by **tear** » Sun Jan 31, 2010 3:48 am

True, though note that most likely one will need to change every* "lib64" reference
to "lib" as x64 Debian keeps 64-bit libs in /lib/ (Ubuntu guys -- please confirm).

I'll be happy to make sure it runs flawlessly on Ubuntu if someone:
a) provides me a way to get into a machine (ssh) (less burden?) or
b) is willing to do several "run these commands and e-mail me the output" iterations

Thanks,
tear

*) target directory name is actually arbitrary but methinks it's better to keep things simple

by **tear** » Wed Apr 07, 2010 6:04 am

EDIT: Jun 19: Following workaround is deprecated. Please use the one from hus -- Ubuntu instructions are located there.

Okay, Ubuntu 10.04 is not exactly the same deal as Fedora 11+. Actually it is, but issue can't be worked
around the same way due to fact of Ubuntu libc.so.6 being stripped more (no STRTAB section).

Fedora 11/12 users please see this post for instructions.

Do the following:

Code: Select all: ## make sure wget, bash, binutils, bc and awk are installed ## log in the user that runs FAH client; this is a MUST, DO NOT USE SUDO cd ~ wget http://darkswarm.org/whosyerdaddy-0.6.sh chmod +x whosyerdaddy-0.6.sh cp -a /lib ~/lib64-fah cd ~/lib64-fah ~/whosyerdaddy-0.6.sh

EDIT, May 14: DO NOT use sudo with any of commands above (unless you run the client as root but that would be... silly);
using sudo (root access) in described procedure but running client as non-root user will get you nowhere -- client will not work;
again, this procedure MUST be performed by the same user that normally runs the client.

Now that you're set up, prepend your client command line with LD_LIBRARY_PATH=~/lib64-fah every time you start the client, for instance

Code: Select all: LD_LIBRARY_PATH=~/lib64-fah ./fah6 -smp 2 -verbosity 9

Reference output follows:

Code: Select all: fah@exp:~$ cat /etc/issue.net Ubuntu lucid (development branch) fah@exp:~$ cd ~ fah@exp:~$ wget http://darkswarm.org/whosyerdaddy-0.6.sh --2010-05-01 07:27:43-- http://darkswarm.org/whosyerdaddy-0.6.sh Resolving darkswarm.org... 85.11.66.60 Connecting to darkswarm.org|85.11.66.60|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 4408 (4.3K) [application/x-sh] Saving to: “whosyerdaddy-0.6.sh” 100%[=======================================================================>] 4,408 --.-K/s in 0.001s 2010-05-01 07:27:43 (3.96 MB/s) - “whosyerdaddy-0.6.sh” saved [4408/4408] fah@exp:~$ chmod +x whosyerdaddy-0.6.sh fah@exp:~$ cp -a /lib ~/lib64-fah cp: cannot create special file `/home/fah/lib64-fah/udev/devices/net/tun': Operation not permitted cp: cannot create special file `/home/fah/lib64-fah/udev/devices/console': Operation not permitted cp: cannot create special file `/home/fah/lib64-fah/udev/devices/loop0': Operation not permitted cp: cannot create special file `/home/fah/lib64-fah/udev/devices/null': Operation not permitted cp: cannot create special file `/home/fah/lib64-fah/udev/devices/ppp': Operation not permitted cp: cannot open `/lib/ufw/user.rules' for reading: Permission denied cp: cannot open `/lib/ufw/user6.rules' for reading: Permission denied fah@exp:~$ cd ~/lib64-fah fah@exp:~/lib64-fah$ ~/whosyerdaddy-0.6.sh whosyerdaddy 0.6, workaround for broken Folding@Home client 6.29 binaries Copyright (c) 2010 by Kris Rusocki <kszysiu@gmail.com> Licensed under GPLv2 Checking for awk bc cat chmod cut dd grep head od readelf sed tac tr ...done. WARNING: no STRTAB, going with 0x30 offset %-| and single-page size. YMMV. DYNSYM at 0x00003c28 processing symbol __rawmemchr Found at position 99 (assuming dynsym) Symbol processed. Perhaps. processing symbol strchr Found at position 1652 (assuming dynsym) Symbol processed. Perhaps. processing symbol strlen Found at position 749 (assuming dynsym) Symbol processed. Perhaps. processing symbol strcpy Found at position 89 (assuming dynsym) Symbol processed. Perhaps. Rebranding shared objects... done. fah@exp:~/lib64-fah$ cd ~/ fah@exp:~$ cd fah fah@exp:~/fah$ LD_LIBRARY_PATH=~/lib64-fah ./fah6 -smp 2 -verbosity 9 Note: Please read the license agreement (fah6 -license). Further use of this software requires that you have read and accepted this agreement. 2 cores detected --- Opening Log file [April 7 04:59:38 UTC] # Linux SMP Console Edition ################################################### ############################################################################### Folding@Home Client Version 6.29 http://folding.stanford.edu ############################################################################### ############################################################################### Launch directory: /home/fah/fah Executable: ./fah6 Arguments: -smp 2 -verbosity 9 [04:59:38] Configuring Folding@Home... User name [Anonymous]? Team Number [0]? Passkey []? Ask before fetching/sending work (no/yes) [no]? Use proxy (yes/no) [no]? Acceptable size of work assignment and work result packets (bigger units may have large memory demands) -- 'small' is <5MB, 'normal' is <10MB, and 'big' is >10MB (small/normal/big) [normal]? big Change advanced options (yes/no) [no]? yes Core Priority (idle/low) [idle]? Disable highly optimized assembly code (no/yes) [no]? Interval, in minutes, between checkpoints (3-30) [15]? Memory, in MB, to indicate (998 available) [998]? Set -advmethods flag always, requesting new advanced scientific cores and/or work units if available (no/yes) [no]? yes Ignore any deadline information (mainly useful if system clock frequently has errors) (no/yes) [no]? Machine ID (1-16) [1]? The following options require you to restart the client before they take effect Disable CPU affinity lock (no/yes) [no]? Additional client parameters []? IP address to bind core to (for viewer) []? [05:00:03] - Ask before connecting: No [05:00:03] - User name: Anonymous (Team 0) [05:00:03] - User ID not found locally [05:00:03] + Requesting User ID from server [05:00:03] - Getting ID from AS: [05:00:03] Connecting to http://assign.stanford.edu:8080/ [05:00:04] Posted data. [05:00:04] Initial: 0C35; - Received User ID = 350C3F556027DD1D [05:00:04] - Machine ID: 1 [05:00:04] [05:00:04] Work directory not found. Creating... [05:00:04] Could not open work queue, generating new queue... [05:00:04] - Preparing to get new work unit... [05:00:04] - Autosending finished units... [April 7 05:00:04 UTC] [05:00:04] Trying to send all finished work units [05:00:04] + No unsent completed units remaining. [05:00:04] - Autosend completed [05:00:04] Cleaning up work directory [05:00:04] + Attempting to get work packet [05:00:04] - Will indicate memory of 998 MB [05:00:04] - Connecting to assignment server [05:00:04] Connecting to http://assign.stanford.edu:8080/ [05:00:04] Posted data. [05:00:04] Initial: ED82; - Successful: assigned to (130.237.232.140). [05:00:04] + News From Folding@Home: Welcome to Folding@Home [05:00:04] Loaded queue successfully. [05:00:04] Connecting to http://130.237.232.140:8080/ [05:00:05] Posted data. [05:00:05] Initial: 0000; - Receiving payload (expected size: 1799542) [05:00:36] - Downloaded at ~56 kB/s [05:00:36] - Averaged speed for that direction ~56 kB/s [05:00:36] + Received work. [05:00:36] + Closed connections [05:00:36] [05:00:36] + Processing work unit [05:00:36] Core required: FahCore_a3.exe [05:00:36] Core not found. [05:00:36] - Core is not present or corrupted. [05:00:36] - Attempting to download new core... [05:00:36] + Downloading new core: FahCore_a3.exe [05:00:36] Downloading core (/~pande/Linux/AMD64/Core_a3.fah from www.stanford.edu) [05:00:36] Initial: AFDE; + 10240 bytes downloaded [05:00:37] Initial: CE21; + 20480 bytes downloaded [05:00:37] Initial: 2CFA; + 30720 bytes downloaded [05:00:37] Initial: B7FB; + 40960 bytes downloaded [05:00:37] Initial: DBFE; + 51200 bytes downloaded [05:00:37] Initial: E913; + 61440 bytes downloaded [05:00:37] Initial: 5064; + 71680 bytes downloaded [05:00:37] Initial: 88C5; + 81920 bytes downloaded [05:00:37] Initial: DA92; + 92160 bytes downloaded [05:00:37] Initial: D441; + 102400 bytes downloaded [05:00:37] Initial: 35C4; + 112640 bytes downloaded [05:00:37] Initial: 8414; + 122880 bytes downloaded [05:00:37] Initial: 8FCC; + 133120 bytes downloaded [05:00:37] Initial: 7D6B; + 143360 bytes downloaded [05:00:37] Initial: A273; + 153600 bytes downloaded [05:00:37] Initial: 45AA; + 163840 bytes downloaded [05:00:37] Initial: FA3C; + 174080 bytes downloaded [05:00:37] Initial: 6729; + 184320 bytes downloaded [05:00:37] Initial: 8533; + 194560 bytes downloaded [05:00:37] Initial: E5B7; + 204800 bytes downloaded [05:00:37] Initial: 0187; + 215040 bytes downloaded [05:00:37] Initial: 1109; + 225280 bytes downloaded [05:00:37] Initial: 8C63; + 235520 bytes downloaded [05:00:37] Initial: 6F6F; + 245760 bytes downloaded [05:00:37] Initial: F54D; + 256000 bytes downloaded [05:00:37] Initial: DCF4; + 266240 bytes downloaded [05:00:37] Initial: C6A4; + 276480 bytes downloaded [05:00:37] Initial: 71B9; + 286720 bytes downloaded [05:00:37] Initial: CC5F; + 296960 bytes downloaded [05:00:37] Initial: 3E8D; + 307200 bytes downloaded [05:00:37] Initial: 5105; + 317440 bytes downloaded [05:00:37] Initial: B423; + 327680 bytes downloaded [05:00:37] Initial: 18C1; + 337920 bytes downloaded [05:00:37] Initial: F2DA; + 348160 bytes downloaded [05:00:37] Initial: 828C; + 358400 bytes downloaded [05:00:37] Initial: E985; + 368640 bytes downloaded [05:00:37] Initial: DBD2; + 378880 bytes downloaded [05:00:37] Initial: 104C; + 389120 bytes downloaded [05:00:37] Initial: 0D8B; + 399360 bytes downloaded [05:00:37] Initial: 78E2; + 409600 bytes downloaded [05:00:37] Initial: 6F2A; + 419840 bytes downloaded [05:00:37] Initial: B2F9; + 430080 bytes downloaded [05:00:37] Initial: 18C6; + 440320 bytes downloaded [05:00:37] Initial: D994; + 450560 bytes downloaded [05:00:37] Initial: D524; + 460800 bytes downloaded [05:00:37] Initial: 1763; + 471040 bytes downloaded [05:00:37] Initial: 9410; + 481280 bytes downloaded [05:00:37] Initial: BBE6; + 491520 bytes downloaded [05:00:37] Initial: ABE4; + 501760 bytes downloaded [05:00:37] Initial: 22D9; + 512000 bytes downloaded [05:00:37] Initial: 4D8B; + 522240 bytes downloaded [05:00:37] Initial: F5B7; + 532480 bytes downloaded [05:00:37] Initial: 108D; + 542720 bytes downloaded [05:00:37] Initial: 074F; + 552960 bytes downloaded [05:00:37] Initial: B2D0; + 563200 bytes downloaded [05:00:37] Initial: 1206; + 573440 bytes downloaded [05:00:37] Initial: 597A; + 583680 bytes downloaded [05:00:37] Initial: 8D92; + 593920 bytes downloaded [05:00:37] Initial: AA03; + 604160 bytes downloaded [05:00:37] Initial: 5301; + 614400 bytes downloaded [05:00:37] Initial: BC09; + 624640 bytes downloaded [05:00:37] Initial: 9067; + 634880 bytes downloaded [05:00:37] Initial: FADB; + 645120 bytes downloaded [05:00:37] Initial: 41BB; + 655360 bytes downloaded [05:00:37] Initial: 793C; + 665600 bytes downloaded [05:00:37] Initial: 60D4; + 675840 bytes downloaded [05:00:37] Initial: A3EA; + 686080 bytes downloaded [05:00:37] Initial: ED0B; + 696320 bytes downloaded [05:00:37] Initial: D093; + 706560 bytes downloaded [05:00:37] Initial: E5B4; + 716800 bytes downloaded [05:00:37] Initial: 3A68; + 727040 bytes downloaded [05:00:37] Initial: 29ED; + 737280 bytes downloaded [05:00:37] Initial: 1380; + 747520 bytes downloaded [05:00:37] Initial: F21F; + 757760 bytes downloaded [05:00:37] Initial: EA3C; + 768000 bytes downloaded [05:00:37] Initial: 6159; + 778240 bytes downloaded [05:00:37] Initial: 4CD8; + 788480 bytes downloaded [05:00:37] Initial: 30CC; + 798720 bytes downloaded [05:00:37] Initial: 2AEF; + 808960 bytes downloaded [05:00:37] Initial: 036D; + 819200 bytes downloaded [05:00:37] Initial: 09A2; + 829440 bytes downloaded [05:00:37] Initial: 10F4; + 839680 bytes downloaded [05:00:37] Initial: 3B9B; + 849920 bytes downloaded [05:00:37] Initial: CC5D; + 860160 bytes downloaded [05:00:37] Initial: 5F3F; + 870400 bytes downloaded [05:00:37] Initial: D3A8; + 880640 bytes downloaded [05:00:37] Initial: CC2B; + 890880 bytes downloaded [05:00:38] Initial: CBAD; + 901120 bytes downloaded [05:00:38] Initial: 6383; + 911360 bytes downloaded [05:00:38] Initial: A020; + 921600 bytes downloaded [05:00:38] Initial: AD06; + 931840 bytes downloaded [05:00:38] Initial: 60B2; + 942080 bytes downloaded [05:00:38] Initial: 4725; + 952320 bytes downloaded [05:00:38] Initial: 1191; + 962560 bytes downloaded [05:00:38] Initial: B786; + 972800 bytes downloaded [05:00:38] Initial: 0A03; + 983040 bytes downloaded [05:00:38] Initial: 26EE; + 993280 bytes downloaded [05:00:38] Initial: 73D9; + 1003520 bytes downloaded [05:00:38] Initial: 012B; + 1013760 bytes downloaded [05:00:38] Initial: CCA4; + 1024000 bytes downloaded [05:00:38] Initial: C4E1; + 1034240 bytes downloaded [05:00:38] Initial: C402; + 1044480 bytes downloaded [05:00:38] Initial: EB24; + 1054720 bytes downloaded [05:00:38] Initial: 7B5A; + 1064960 bytes downloaded [05:00:38] Initial: 78FF; + 1075200 bytes downloaded [05:00:38] Initial: AF0F; + 1085440 bytes downloaded [05:00:38] Initial: D54A; + 1095680 bytes downloaded [05:00:38] Initial: D564; + 1105920 bytes downloaded [05:00:38] Initial: 090A; + 1116160 bytes downloaded [05:00:38] Initial: D518; + 1126400 bytes downloaded [05:00:38] Initial: F5FD; + 1136640 bytes downloaded [05:00:38] Initial: FA96; + 1146880 bytes downloaded [05:00:38] Initial: D03A; + 1157120 bytes downloaded [05:00:38] Initial: 7759; + 1167360 bytes downloaded [05:00:38] Initial: E364; + 1177600 bytes downloaded [05:00:38] Initial: AB77; + 1187840 bytes downloaded [05:00:38] Initial: 376D; + 1198080 bytes downloaded [05:00:38] Initial: E0EF; + 1208320 bytes downloaded [05:00:38] Initial: 166C; + 1218560 bytes downloaded [05:00:38] Initial: EF31; + 1228800 bytes downloaded [05:00:38] Initial: 3707; + 1239040 bytes downloaded [05:00:38] Initial: 7A08; + 1249280 bytes downloaded [05:00:38] Initial: 22D0; + 1259520 bytes downloaded [05:00:38] Initial: 1925; + 1269760 bytes downloaded [05:00:38] Initial: 1494; + 1280000 bytes downloaded [05:00:38] Initial: 2D84; + 1290240 bytes downloaded [05:00:38] Initial: 3538; + 1300480 bytes downloaded [05:00:38] Initial: 6272; + 1310720 bytes downloaded [05:00:38] Initial: FF61; + 1320960 bytes downloaded [05:00:38] Initial: 5A14; + 1331200 bytes downloaded [05:00:38] Initial: 01E5; + 1341440 bytes downloaded [05:00:38] Initial: 942C; + 1351680 bytes downloaded [05:00:38] Initial: A87E; + 1361920 bytes downloaded [05:00:38] Initial: D6A0; + 1372160 bytes downloaded [05:00:38] Initial: 3604; + 1382400 bytes downloaded [05:00:38] Initial: EAAF; + 1392640 bytes downloaded [05:00:38] Initial: A416; + 1402880 bytes downloaded [05:00:38] Initial: F7E0; + 1413120 bytes downloaded [05:00:38] Initial: 3D28; + 1423360 bytes downloaded [05:00:38] Initial: 1D3D; + 1433600 bytes downloaded [05:00:38] Initial: 3A0D; + 1443840 bytes downloaded [05:00:38] Initial: 9050; + 1454080 bytes downloaded [05:00:38] Initial: D0D8; + 1464320 bytes downloaded [05:00:38] Initial: A4B3; + 1474560 bytes downloaded [05:00:38] Initial: 69A0; + 1484800 bytes downloaded [05:00:38] Initial: 042A; + 1495040 bytes downloaded [05:00:38] Initial: DCF2; + 1505280 bytes downloaded [05:00:38] Initial: 6BC7; + 1515520 bytes downloaded [05:00:38] Initial: A79C; + 1525760 bytes downloaded [05:00:38] Initial: 483A; + 1536000 bytes downloaded [05:00:38] Initial: 909D; + 1546240 bytes downloaded [05:00:38] Initial: 5CB1; + 1556480 bytes downloaded [05:00:38] Initial: C021; + 1566720 bytes downloaded [05:00:38] Initial: 23A0; + 1576960 bytes downloaded [05:00:38] Initial: 2165; + 1587200 bytes downloaded [05:00:38] Initial: 294B; + 1597440 bytes downloaded [05:00:38] Initial: 2396; + 1607680 bytes downloaded [05:00:38] Initial: 34DF; + 1617920 bytes downloaded [05:00:38] Initial: 04EE; + 1628160 bytes downloaded [05:00:38] Initial: 41D5; + 1638400 bytes downloaded [05:00:38] Initial: B118; + 1648640 bytes downloaded [05:00:38] Initial: 7E76; + 1658880 bytes downloaded [05:00:38] Initial: 335A; + 1669120 bytes downloaded [05:00:38] Initial: E80B; + 1679360 bytes downloaded [05:00:38] Initial: A281; + 1689600 bytes downloaded [05:00:38] Initial: B4A1; + 1699840 bytes downloaded [05:00:38] Initial: 36DF; + 1710080 bytes downloaded [05:00:38] Initial: 32A3; + 1720320 bytes downloaded [05:00:38] Initial: C271; + 1730560 bytes downloaded [05:00:38] Initial: B8EE; + 1740800 bytes downloaded [05:00:38] Initial: 97D7; + 1751040 bytes downloaded [05:00:38] Initial: F0C8; + 1761280 bytes downloaded [05:00:38] Initial: 72C1; + 1771520 bytes downloaded [05:00:38] Initial: 461E; + 1781760 bytes downloaded [05:00:38] Initial: F898; + 1792000 bytes downloaded [05:00:38] Initial: BE10; + 1802240 bytes downloaded [05:00:38] Initial: CF05; + 1812480 bytes downloaded [05:00:38] Initial: CE0A; + 1822720 bytes downloaded [05:00:38] Initial: CD7B; + 1832960 bytes downloaded [05:00:38] Initial: 5C2F; + 1843200 bytes downloaded [05:00:38] Initial: 4E25; + 1853440 bytes downloaded [05:00:38] Initial: CC07; + 1863680 bytes downloaded [05:00:38] Initial: BE89; + 1873920 bytes downloaded [05:00:38] Initial: 2B01; + 1884160 bytes downloaded [05:00:38] Initial: C7AF; + 1885206 bytes downloaded [05:00:38] Verifying core Core_a3.fah... [05:00:38] Signature is VALID [05:00:38] [05:00:38] Trying to unzip core FahCore_a3.exe [05:00:38] Decompressed FahCore_a3.exe (4415280 bytes) successfully [05:00:38] + Core successfully engaged [05:01:02] [05:01:02] + Processing work unit [05:01:02] Core required: FahCore_a3.exe [05:01:02] Core found. [05:01:02] Working on queue slot 01 [April 7 05:01:02 UTC] [05:01:02] + Working ... [05:01:02] - Calling './FahCore_a3.exe -dir work/ -nice 19 -suffix 01 -np 2 -checkpoint 15 -verbose -lifeline 10668 -version 629' [05:01:03] [05:01:03] *------------------------------* [05:01:03] Folding@Home Gromacs SMP Core [05:01:03] Version 2.17 (March 6, 2010) [05:01:03] [05:01:03] Preparing to commence simulation [05:01:03] - Looking at optimizations... [05:01:03] - Created dyn [05:01:03] - Files status OK [05:01:03] - Expanded 1799030 -> 2392545 (decompressed 132.9 percent) [05:01:03] Called DecompressByteArray: compressed_data_size=1799030 data_size=2392545, decompressed_data_size=2392545 diff=0 [05:01:03] - Digital signature verified [05:01:03] [05:01:03] Project: 6015 (Run 0, Clone 222, Gen 34) [05:01:03] [05:01:03] Assembly optimizations on if available. [05:01:03] Entering M.D. Starting 2 threads NNODES=2, MYRANK=0, HOSTNAME=thread #0 NNODES=2, MYRANK=1, HOSTNAME=thread #1 Reading file work/wudata_01.tpr, VERSION 4.0.99_development_20090605 (single precision) Note: tpx file_version 68, software version 70 Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'Protein in POPC' 17500002 steps, 35000.0 ps (continuing from step 17000002, 34000.0 ps). [05:01:10] Completed 0 out of 500000 steps (0%)

Enjoy!

tear

EDIT: technical & editorial updates
EDIT: 0.6 -- added pre-requisite checks (and improved instructions per p2501's suggestion)

by **hrsetrdr** » Sat Apr 24, 2010 11:35 pm

I just installed Ubuntu 10.04rc, used the "whosyerdaddy" with the following results:

Code: Select all: hrsetrdr@asrock3:~/lib64-fah$ ~/whosyerdaddy-0.5.sh whosyerdaddy 0.5, a workaround for broken Folding@Home client 6.29 binaries Copyright (c) 2010 by Kris Rusocki <kszysiu@gmail.com> Licensed under GPLv2 WARNING: no STRTAB, going with 0x30 offset %-| and single-page size. YMMV. DYNSYM at 0x00003c28 processing symbol __rawmemchr Found at position 99 (assuming dynsym) WARNING: not an IFUNC symbol! Doing nothing. processing symbol strchr Found at position 1652 (assuming dynsym) WARNING: not an IFUNC symbol! Doing nothing. processing symbol strlen Found at position 749 (assuming dynsym) WARNING: not an IFUNC symbol! Doing nothing. processing symbol strcpy Found at position 89 (assuming dynsym) WARNING: not an IFUNC symbol! Doing nothing. Rebranding shared objects...

I still get the following error:

Code: Select all: fah6: relocation error: /lib/libnss_files.so.2: symbol __rawmemchr, version GLIBC_2.2.5 not defined in file libc.so.6 with link time reference

...not sure where to take it from here.

by **tear** » Sun Apr 25, 2010 6:14 am

Hey hrsetrdr, thanks for the report.

Geez. That seems to be significant difference for a transition from beta to rc (can you say code freeze?).

Can you tell me what "sudo dpkg -s libc6 | grep Version" returns?

I'll take a look at it once I'm done with my (long overdue) dinner.

Thanks!
tear

EDIT: language and command fixup

by **tear** » Sun Apr 25, 2010 7:16 am

Duh. Silly me. These messages may also indicate you've already run the script.

To be on a safe side, can you please remove ~/lib64-fah directory (with "rm -fr ~/lib64-fah"),
start from scratch and see if you still get same output?

I've updated glibc to 2.11.1-0ubuntu7 and am _not_ geting these messages.

Thanks,
tear

by **Jeff-M** » Mon Apr 26, 2010 5:23 pm

tear wrote:Do the following:
Code: Select all
## make sure bash, wget, binutils and awk are installed ## log in the user that runs FAH client cd ~ wget http://darkswarm.org/whosyerdaddy-0.5.sh chmod +x whosyerdaddy-0.5.sh cp -a /lib ~/lib64-fah cd ~/lib64-fah ~/whosyerdaddy-0.5.sh

Now that you're set up, prepend your client command line with LD_LIBRARY_PATH=~/lib64-fah every time you start the client, for instance:
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LD_LIBRARY_PATH=~/lib64-fah ./fah6 -smp 2 -verbosity 9

Worked for me on ubuntu 10.04RC. We'll see what happens after the first WU is completed.

by **p2501** » Sat May 01, 2010 9:21 am

Thank you alot for this fix, tear. I updated my dedicated folder/server from 9.10 to the new LTS an hour ago, not knowing that there's a glitch in glibc linkage. After successfully applying your work-around it's running full blast now again, thanks to you. My system was missing bc though, dunno if that is common. Maybe add it to the "Make sure..." line?!

:-)

by **tear** » Sat May 01, 2010 1:53 pm

With you it's always a pleasure

Re bc
Weird... so it seems either bc is not installed (by default) with server LTS
or there was general change between beta and release versions (honestly,
I don't feel like investigating this:)

Let me add some sanity checks for pre-requisites. 0.6 is in the works.

Thanks for feedback!

tear

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