Re: [ccp4bb] raid array load question
Interesting and simple way to test the write performance. Simultaneous
writes could then be tested by putting an ampersand ('') at the end of
the 'dd' command, couldn't they? And if you get tired of typing all the
number, you could use the 'seq' command instead.
Cheers, Tim
/bin/tcsh
set time
foreach file ( 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 )
dd if=/dev/zero bs=2G count=1 of=/home/username/deleteme$file
end
-James Holton
MAD Scientist
Harry M. Greenblatt wrote:
BSD
To those hardware oriented:
We have a compute cluster with 23 nodes (dual socket, dual core Intel
servers). Users run simulation jobs on the nodes from the head node. At
the end of each simulation, a result file is compressed to 2GB, and copied
to the file server for the cluster (not the head node) via NFS. Each node
is connected via a Gigabit line to a switch. The file server has a 4-link
aggregated Ethernet trunk (4Gb/S) to the switch. The file server also has
two sockets, with Dual Core Xeon 2.1GHz CPU's and 4 GB of memory, running
RH4. There are two raid arrays (RAID 5), each consisting of 8x500GB SATA
II WD server drives, with one file system on each. The raid cards are AMCC
3WARE 9550 and 9650SE (PCI-Express) with 256 MB of cache memory .
When several (~10) jobs finish at once, and the nodes start copying the
compressed file to the file server, the load on the file server gets very
high (~10), and the users whose home directory are on the file server
cannot work at their stations. Using nmon to locate the bottleneck, it
appears that disk I/O is the problem. But the numbers being reported are a
bit strange. It reports a throughput of only about 50MB/s, and claims the
disk is 100% busy. These raid cards should give throughput in the
several hundred MB/s range, especially the 9650 which is rated at 600MB/s
RAID 6 write (and we have RAID 5).
1) Is there a more friendly system load monitoring tool we can use?
2) The users may be able to stagger the output schedule of their jobs, but
based on the numbers, we get the feeling the RAID arrays are not performing
as they should. Any suggestions?
Thanks
Harry
-
Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
Weizmann Institute of SciencePhone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel
Re: [ccp4bb] raid array load question
Woops! Yes, of course you would want an ampersand in my little
pseudo-script to background the dd jobs. My mistake. seq is also
one of my favorite commands, but some systems are so stripped-down that
they don't have it!
-James
Tim Gruene wrote:
Interesting and simple way to test the write performance. Simultaneous
writes could then be tested by putting an ampersand ('') at the end
of the 'dd' command, couldn't they? And if you get tired of typing all
the number, you could use the 'seq' command instead.
Cheers, Tim
/bin/tcsh
set time
foreach file ( 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
22 23 )
dd if=/dev/zero bs=2G count=1 of=/home/username/deleteme$file
end
-James Holton
MAD Scientist
Harry M. Greenblatt wrote:
BSD
To those hardware oriented:
We have a compute cluster with 23 nodes (dual socket, dual core
Intel servers). Users run simulation jobs on the nodes from the
head node. At the end of each simulation, a result file is
compressed to 2GB, and copied to the file server for the cluster
(not the head node) via NFS. Each node is connected via a Gigabit
line to a switch. The file server has a 4-link aggregated Ethernet
trunk (4Gb/S) to the switch. The file server also has two sockets,
with Dual Core Xeon 2.1GHz CPU's and 4 GB of memory, running RH4.
There are two raid arrays (RAID 5), each consisting of 8x500GB SATA
II WD server drives, with one file system on each. The raid cards
are AMCC 3WARE 9550 and 9650SE (PCI-Express) with 256 MB of cache
memory . When several (~10) jobs finish at once, and the nodes
start copying the compressed file to the file server, the load on
the file server gets very high (~10), and the users whose home
directory are on the file server cannot work at their stations.
Using nmon to locate the bottleneck, it appears that disk I/O is the
problem. But the numbers being reported are a bit strange. It
reports a throughput of only about 50MB/s, and claims the disk is
100% busy. These raid cards should give throughput in the several
hundred MB/s range, especially the 9650 which is rated at 600MB/s
RAID 6 write (and we have RAID 5).
1) Is there a more friendly system load monitoring tool we can use?
2) The users may be able to stagger the output schedule of their
jobs, but based on the numbers, we get the feeling the RAID arrays
are not performing as they should. Any suggestions?
Thanks
Harry
-
Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
Weizmann Institute of SciencePhone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel
[ccp4bb] wich program to test an alternative phaser solution
Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters (found in the .sol file) to generate the alternative solution? Thank you in advance, Fred.
Re: [ccp4bb] wich program to test an alternative phaser solution
PDBSET xyzin model.pdb ROTA EULER a b c SHIFT FRAC tx ty tz CELL new cell end Vellieux wrote: Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters (found in the .sol file) to generate the alternative solution? Thank you in advance, Fred.
Re: [ccp4bb] wich program to test an alternative phaser solution
Hi Fred, in future PHASER runs you can also ask the program to write out an X number of the top solutions as separate coordinate files via the keyword TOPFILES (e.g 'TOPFILES 10' for the top ten solutions). In the PHASER GUI you can enter that request in the 'Define Data' block. best wishes, Savvas Savvas N. Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Vellieux Sent: Tuesday, January 15, 2008 10:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] wich program to test an alternative phaser solution Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters (found in the .sol file) to generate the alternative solution? Thank you in advance, Fred.
[ccp4bb] raid array load comments
BSD Thank you to all the respondents. Some comments: 1. Some believe that the write performance in RAID 5 is only as good as performance to one disk. This is true only in RAID 3 (under certain conditions), where parity is written as a separate operation to one dedicated parity disk. With distributed parity in RAID 5 this bottleneck is overcome, and write performance is better than single disk limits. 2. These are SATA II drives which are rated at 3Gb/s, or 375MB/s; even if single-drive I/O limits were a problem, we are not reaching this value. I think James Holton's suggestions are more on the mark. We will try and investigate. Thanks Harry On Jan 15, 2008, at 9:54 AM, James Holton wrote: Ahh, there is nothing quite like a nice big cluster to bring any file server to its knees. - Harry M. Greenblatt Staff Scientist Dept of Structural Biology [EMAIL PROTECTED] Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
Re: [ccp4bb] PERL system call to CCP4
Hi,
Here is a copy of the occp4.pm file which we use at the PDB Depositions
and Processing Site at the EBI. This perl module works and can be
called as following:
#/bin/perl
require '/ebi/msd/work2/msdsd/production/x86_64/lib/site_perl/occp4.pm';
my $sfcheck = new occp4('sfcheck','hklin'=$sf,'xyzin'=$pdb);
$sfcheck-logfile(sfcheck_$pdbid.log);
$sfcheck-keywords(LABIN=I=I SIGI=SIGI);
error(sfcheck did not complete properly, check $sflog file) if
($sfcheck-run());
Hope it helps.
Jawahar Swaminathan
[EMAIL PROTECTED] wrote:
Dear CCP4 users,
I am writing a PERL script to execute a number of CCP4 commands (ncsmask,
pdbset, and dm) in succession. I have tried using system call or PIPE
command, neither of which work. The ccp4 scripts generated work independently
on the command line.
Any suggestions?
Thank you in advance!
#!/ebi/msd/bin/perl
#
# $Id: occp4.pm,v 1.5 1999/02/08 08:35:42 manu Exp $
#
# $Log: occp4.pm,v $
# Revision 1.5 1999/02/08 08:35:42 manu
# added copyright notice
#
# Revision 1.4 1998/09/14 13:20:04 manu
# documentation
#
# Revision 1.3 1998/09/14 10:08:18 manu
# split_pdb
#
# Revision 1.2 1998/08/31 14:24:36 manu
# minor changes in documentation
#
# Revision 1.1 1998/08/31 13:42:58 manu
# Initial revision
#
# This is occp4.pm, an object-oriented perl module for writing ccp4 scripts
# Copyright (C) 1999 Emmanuel Courcelle Jean-Pierre Samama
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
#
# New versions should be available on ftp://ftp.ipbs.fr
# Comments are to be sent to [EMAIL PROTECTED]
#
=head1 NAME
occp4.pm - Object oriented CCP4 module
=head1 DESCRIPTION
This module is VERY useful when you want to use ccp4 programs from within
a perl script. The ccp4 environment Imust be loaded before the script is
started.
=head1 The constructors
$ccp4_obj = new OCCP4('prgm_name',log1=file1,log2=file2,...);
B'prgm_name' is the name of a ccp4 program.
Blog1=Egtfile1 are pairs of logical names/real names, used by the
ccp4 programs for specifying the input/output files. Those parameters are
optional, and may be overriden with the iofiles (see Liofiles, iofildel
member function).
=head1 The destructor
When the memory allocated for the object is returned to the system (at the end
of the block, or more generally when no reference points to that object, see
perl documentation for the details),
a destructor is called. Its only action is to unlink the temporary files
which did belong to this object.
If the debug flag 'F' is specified, the files are Inot unlinked, but a
message is printed to the standard output.
=head1 The member functions
Following paragraphs describe the member functions available from every object.
=head2 keywords, keywdel, keywrep
(1) $ccp4_obj-keywords(keyw1=val1,keyw2=val2,...)
(2) $value=$ccp4_obj-keywords('keyword')
(3) @value=$ccp4_obj-keywords('keyword')
(4) @keywords=$ccp4_obj-keywords()
(5) $ccp4_obj-keywdel('keyw1','keyw2')
(6) $ccp4_obj-keywrep(keyw1=val1,keyw2=val2)
You must use (1) to set the value of one or several keywords.
If the function is called and this keyword is already defined,
the new value is 'appended', ie the same keyword may appear several times.
(2) is used to retrieve the value of one specific keyword. If the keyword
appears several times, Bonly the first occurrence of the keyword will be
retrieved this way. If you want to retrieve Ball occurrences of a specific
keyword, use (3). (4) is used to retrieve all the keyword/value pairs in one
operation. (5) The keywdel function is used to delete Ball occurrences of
one given keyword. (6) The keywrep function deletes Ball occurrences of
the specified keywords, and replaces them with the values passed by parameters.
See also LSpecial values, Linput_file, input_string, input_src,
LThe KCCP4 and LCCP4 global variables.
=head2 iofiles, iofildel
(1) $ccp4_obj-iofiles(HKLIN=$file1,HKLOUT=$file2,...)
(2) $file=$ccp4_obj-iofiles('HKLIN')
(3) %files=$ccp4_obj-iofiles()
(4) $ccp4_obj-iofildel('HKLIN')
(1) is used to set or change the value of a logical name for the input or
output files (they can also. (2) is used to retrieve the value of a
logical name. (3) is used to retrieve all logical name/real name pairs.
(4) iofildel is used to delete one logical name from the list of iofiles.
See also
Re: [ccp4bb] wich program to test an alternative phaser solution
As suggested earlier, you can use the TOPFILES command to get Phaser to produce the files for more solutions. However, instead of rerunning the whole job, you can produce the PDB files alone by feeding the .sol file into a packing (MR_PAK) job, or both PDB and MTZ files by feeding the .sol file into a rescoring (MR_LLG) job. Randy Read On Jan 15 2008, Vellieux wrote: Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters (found in the .sol file) to generate the alternative solution? Thank you in advance, Fred.
[ccp4bb] Post-doctoral/Research Associate Position Available
NIH Funded position for studies on studies on the yeast ATP synthase. Studies on mutant forms of the F1 ATPase and on the F1Fo ATP synthase. The candidate must have a PhD, or the equivalent, with research experience in Biochemistry, Biophysics, Structural Biology, or Molecular Biology. See: http://rosalindfranklin.edu/cms/biochem/dm_index.html for details. David Mueller Biochemistry and Molecular Biology Rosalind Franklin University of Medicine and Science Greenbay Road North Chicago, IL 60064 [EMAIL PROTECTED] http://www.rosalindfranklin.edu/cms/biochem/mueller.html Tel: 847-578-8606 FAX: 847-578-3240
Re: [ccp4bb] Perl
Hi, thanks for all the help! system (source ccp4.setup) does the trick, every time before a ccp4 script is called, the environmental parameters have to be set up this way. Quoting Ed Hoeffner [EMAIL PROTECTED]: Hi You don't include any error messages, so it's very difficult to troubleshoot. However, as a wild guess, I'd suggest you ensure that you execute the ccp4 setup file and then try your command. I don't know perl, but the call might look something like system(source ccp4.setup ; pdbset ...). As I recall, there is a ccp4 setup file that has to be loaded first, though you may have to find it and adjust that part of the command accordingly so the file can be located. Ed --
[ccp4bb] CCP4 workshop in US, 2nd announcement
Dear Colleagues, This is second announcement of the CCP4 workshop. WHAT CCP4 school: From data processing to structure refinement and beyond. WHERE Advanced Photon Source, Argonne National Laboratory, near Chicago, USA. ORGANIZERS CCP4, University of York, GM/CA-CAT Argonne PROGRAM Lectures in the morning, tutorials in the afternoon, hands-on trouble shooting in the evening. Registered student are encouraged to bring their own problem data. COVERED SOFTWARE INCLUDES Mosflm, Scala, HKL2000, Refmac, ArpWarp, PHENIX, Phaser, Coot, SHELXC/D/E, Balbes, Mrbump, Buccaneer, more PARTICIPANTS Young scientists with basic knowledge of CCP4. Up to 20 registered students will be provided with computers and will participate in hands-on session. Others are welcome to listen to lectures FEES There are no registration fees. Meals and hotel will be covered by the organizers. Students will pay only for their transportation DEADLINE Applications will be accepted until March 31. Selection of students will be made and notifications sent within two weeks after that. APPLICATIONS together with the letter of support from the supervisor should be sent to Nukri ([EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ) or Garib ([EMAIL PROTECTED]) or Ronan ([EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ) Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Re: [ccp4bb] CCP4 workshop in US, 2nd announcement
The workshop will be held from May 23 through 28, 2008. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sanishvili, Ruslan Sent: Tuesday, January 15, 2008 3:07 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 workshop in US, 2nd announcement Dear Colleagues, This is second announcement of the CCP4 workshop. WHAT CCP4 school: From data processing to structure refinement and beyond. WHERE Advanced Photon Source, Argonne National Laboratory, near Chicago, USA. ORGANIZERS CCP4, University of York, GM/CA-CAT Argonne PROGRAM Lectures in the morning, tutorials in the afternoon, hands-on trouble shooting in the evening. Registered student are encouraged to bring their own problem data. COVERED SOFTWARE INCLUDES Mosflm, Scala, HKL2000, Refmac, ArpWarp, PHENIX, Phaser, Coot, SHELXC/D/E, Balbes, Mrbump, Buccaneer, more PARTICIPANTS Young scientists with basic knowledge of CCP4. Up to 20 registered students will be provided with computers and will participate in hands-on session. Others are welcome to listen to lectures FEES There are no registration fees. Meals and hotel will be covered by the organizers. Students will pay only for their transportation DEADLINE Applications will be accepted until March 31. Selection of students will be made and notifications sent within two weeks after that. APPLICATIONS together with the letter of support from the supervisor should be sent to Nukri ([EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ) or Garib ([EMAIL PROTECTED]) or Ronan ([EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ) Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
[ccp4bb] Calculating volume of Ligands
Hi All, Can anyone tell me any program that calculates voume of a ligand? Moreover, is there also any program that can calculate the volume of a ligand from its coordinates? Thanks, Rajan.
Re: [ccp4bb] crystallisation robot
Dear Alexey, being involved in the development of the 'fixed needles + a few' robots and 96-well plates early on, I wonder about your bad experiences. You seem to say that the Phoenix requires more maintenance than the Mosquito - how long have you had that Phoenix or what model is giving you the trouble? For the electrostatics issue: it’s the plates that are electrostatic not the robot. This is a common lament for plastic plate users, and the Intelliplate designed to go with the Phoenix comes in anti-static bags as used in electronic component packaging. Other plates have anti-static coating, and there may be other tricks as well to avoid electrostatic charge (comments anyone?) Also, the limitation of the 200+200 you claim for the Phoenix seems extreme, users have set up 200+200 already with the old hydra+1 contraptions, and 100+100 seems to work reliable with the Phoenix (maybe some users can comment?). Could it be that yours is not set up correctly? I am sure ARI will be happy to send a European rep by to check. Best regards, BR -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Alexey Rak Sent: Monday, January 14, 2008 9:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallisation robot we have recently tried the new lid mentioned below. It works very well, Mosquito makes 3 hanging drops 96 well plate in 3-4 minutes! The film is very easy to handle and it is very transparent. The price for the lid is significantly reduced: from 13€ before to 4€ now. Comparing to Cartesian and Phoenix robots the Mosquito is REALLY maintenance free machine, especially the third generation insect where many 1st and 2nd Mosquito generation users advices have been implicated. Alexey Rak Structural Biology, Chemical Sciences Sanofi-Aventis Centre de Recherche Paris
Re: [ccp4bb] Calculating volume of Ligands
ccp4 includes a program called 'volume' that does this. see 'man volume' for a description, or $CCP4/html/volume.html Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 15 Jan 2008, Rajan Pillai wrote: Hi All, Can anyone tell me any program that calculates voume of a ligand? Moreover, is there also any program that can calculate the volume of a ligand from its coordinates? Thanks, Rajan.
