installing pymol in centos 6

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bharat_46010
Posts: 5
Joined: 2013/04/21 02:47:45

installing pymol in centos 6

Post by bharat_46010 » 2013/04/21 02:51:05

Hi,

I am trying to install pymol in centos 6, using the command yum -y install pymol . I am getting the following error :-

[root@bme peptide EGDT]# yum -y install pymol
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package pymol.x86_64 0:1.5.0.2-7.20120218svn3982.el6 will be installed
--> Processing Dependency: python-pmw for package: pymol-1.5.0.2-7.20120218svn3982.el6.x86_64
--> Processing Dependency: glew for package: pymol-1.5.0.2-7.20120218svn3982.el6.x86_64
--> Processing Dependency: apbs for package: pymol-1.5.0.2-7.20120218svn3982.el6.x86_64
--> Processing Dependency: libGLEW.so.1.5()(64bit) for package: pymol-1.5.0.2-7.20120218svn3982.el6.x86_64
--> Running transaction check
---> Package apbs.x86_64 0:1.2.1-4.el6 will be installed
--> Processing Dependency: python-ZSI for package: apbs-1.2.1-4.el6.x86_64
--> Processing Dependency: libmaloc.so.1()(64bit) for package: apbs-1.2.1-4.el6.x86_64
--> Processing Dependency: libf77blas.so.3()(64bit) for package: apbs-1.2.1-4.el6.x86_64
--> Processing Dependency: libblas.so.3()(64bit) for package: apbs-1.2.1-4.el6.x86_64
--> Processing Dependency: libatlas.so.3()(64bit) for package: apbs-1.2.1-4.el6.x86_64
---> Package glew.x86_64 0:1.5.5-1.el6 will be installed
---> Package python-pmw.noarch 0:1.3.2-9.el6 will be installed
--> Processing Dependency: tkinter for package: python-pmw-1.3.2-9.el6.noarch
--> Running transaction check
---> Package apbs.x86_64 0:1.2.1-4.el6 will be installed
--> Processing Dependency: libf77blas.so.3()(64bit) for package: apbs-1.2.1-4.el6.x86_64
--> Processing Dependency: libblas.so.3()(64bit) for package: apbs-1.2.1-4.el6.x86_64
--> Processing Dependency: libatlas.so.3()(64bit) for package: apbs-1.2.1-4.el6.x86_64
---> Package maloc.x86_64 0:0.2-4.el6 will be installed
---> Package python-ZSI.noarch 0:2.0-6.el6 will be installed
---> Package python-pmw.noarch 0:1.3.2-9.el6 will be installed
--> Processing Dependency: tkinter for package: python-pmw-1.3.2-9.el6.noarch
--> Finished Dependency Resolution
Error: Package: apbs-1.2.1-4.el6.x86_64 (epel)
Requires: libf77blas.so.3()(64bit)
Error: Package: python-pmw-1.3.2-9.el6.noarch (epel)
Requires: tkinter
Error: Package: apbs-1.2.1-4.el6.x86_64 (epel)
Requires: libblas.so.3()(64bit)
Error: Package: apbs-1.2.1-4.el6.x86_64 (epel)
Requires: libatlas.so.3()(64bit)
You could try using --skip-broken to work around the problem
** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Client)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Delta)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs = ('1', '1.7.17', '26.el6')
opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of perl(Ace::Browser::LocalSiteDefs)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Apache::DBI)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::ASN1::EntrezGene)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Expression::Contact)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Expression::DataSet)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Expression::Platform)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Expression::Sample)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Phylo::Factory)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Phylo::Forest::Tree)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Phylo::IO)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Phylo::Matrices)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Phylo::Matrices::Datum)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Bio::Phylo::Matrices::Matrix)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Convert::Binary::C)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(DBD::Pg)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(PostScript::TextBlock)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Test::Exception)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(Test::Warn)
opt-perl-BioPerl-DB-1.006900-0.el6.noarch has missing requires of perl(DBD::Oracle)
opt-perl-BioPerl-Run-1.006900-0.el6.noarch has missing requires of perl(Bio::Tools::Run::StandAloneBlastPlus::BlastMethods)
opt-perl-BioPerl-Run-1.006900-0.el6.noarch has missing requires of perl(Bio::Tools::Run::WrapperBase::CommandExts)
opt-perl-Cache-Cache-1.06-0.el6.noarch has missing requires of perl(IPC::ShareLite)
opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of perl(Coro)
opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of perl(Coro::Handle)
opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of perl(Coro::Select)
opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of perl(RPC::PlClient) >= ('0', '0.2000', None)
opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of perl(RPC::PlServer) >= ('0', '0.2001', None)
opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of perl(Win32::ODBC)
opt-perl-Data-Stag-0.11-0.el6.x86_64 has missing requires of perl(Tk)
opt-perl-Data-Stag-0.11-0.el6.x86_64 has missing requires of perl(Tk::Label)
opt-perl-Data-Stag-0.11-0.el6.x86_64 has missing requires of perl(Tk::Tree)
opt-perl-Digest-Perl-MD5-1.8-0.el6.noarch has missing requires of /usr/bin/false
opt-perl-HTTP-Cookies-6.01-0.el6.noarch has missing requires of perl(Win32)
opt-perl-IPC-Run-0.92-0.el6.noarch has missing requires of perl(Win32::Process)
opt-perl-IPC-Run-0.92-0.el6.noarch has missing requires of perl(Win32API::File)
opt-perl-MLDBM-2.04-0.el6.noarch has missing requires of perl(FreezeThaw)
opt-perl-Moose-2.0604-0.el6.x86_64 has missing requires of perl(Moose::Conflicts)
opt-perl-Moose-2.0604-0.el6.x86_64 has missing requires of perl(Moose::Error::Util)
opt-perl-Package-Stash-0.33-0.el6.noarch has missing requires of perl(Package::Stash::Conflicts)
opt-perl-SOAP-Lite-0.715-0.el6.noarch has missing requires of perl(MIME::Lite)
opt-perl-SOAP-Lite-0.715-0.el6.noarch has missing requires of perl(SOAP::Transport::TCP)
opt-perl-Spreadsheet-ParseExcel-0.59-0.el6.noarch has missing requires of perl(Jcode)
opt-perl-Spreadsheet-ParseExcel-0.59-0.el6.noarch has missing requires of perl(Spreadsheet::WriteExcel)
opt-perl-Spreadsheet-ParseExcel-0.59-0.el6.noarch has missing requires of perl(Unicode::Map)
opt-perl-XML-SAX-0.99-0.el6.noarch has missing requires of perl(XML::SAX::PurePerl::DTDDecls)
opt-perl-XML-SAX-0.99-0.el6.noarch has missing requires of perl(XML::SAX::PurePerl::DocType)
opt-perl-XML-SAX-0.99-0.el6.noarch has missing requires of perl(XML::SAX::PurePerl::EncodingDetect)
opt-perl-XML-SAX-0.99-0.el6.noarch has missing requires of perl(XML::SAX::PurePerl::XMLDecl)
opt-perl-YAML-0.84-0.el6.noarch has missing requires of perl(Test::Base) >= ('0', '0.47', None)
opt-perl-YAML-0.84-0.el6.noarch has missing requires of perl(Test::Base::Filter)
opt-perl-libwww-perl-6.04-0.el6.noarch has missing requires of perl(Authen::NTLM)
opt-perl-libwww-perl-6.04-0.el6.noarch has missing requires of perl(HTTP::GHTTP)





Can anybody help me in solving the error ??

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toracat
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installing pymol in centos 6

Post by toracat » 2013/04/21 06:10:04

I have been running pymol (from EPEL) on an RHEL-6 box, so it should install just fine on CentOS 6.

Your output shows (for example):
[quote]
Error: Package: python-pmw-1.3.2-9.el6.noarch (epel)
Requires: tkinter
[/quote]
tkinter is available from CentOS. What do you see with a 'yum list tkinter' ? When you ran 'yum -y install pymol', were all the distro repos available?

bharat_46010
Posts: 5
Joined: 2013/04/21 02:47:45

Re: installing pymol in centos 6

Post by bharat_46010 » 2013/04/21 07:01:29

Hi,

When I use the command : yum list tkinter , it gives the error : Error: No matching Packages to list . Therefore, I tried installing tkinter , I get the error for missing libTix.so file and when I try installing it , it gvies another error : libX11.so.6 is needed by tix-1:8.4.3-7.fc17.i686 . However, libX11 is already installed in my sytem. ??

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toracat
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Posts: 7280
Joined: 2006/09/03 16:37:24
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Contact:

Re: installing pymol in centos 6

Post by toracat » 2013/04/21 11:06:17

Please follow the instructions on [url=https://www.centos.org/modules/newbb/viewtopic.php?topic_id=28723&forum=54]How to Provide Information About Your System[/url] and provide the output returned by [b]getinfo.sh packages[/b] .

bharat_46010
Posts: 5
Joined: 2013/04/21 02:47:45

Re: installing pymol in centos 6

Post by bharat_46010 » 2013/04/22 03:36:37

Information for general problems.
[code]
== BEGIN uname -rmi ==
2.6.32-279.14.1.el6.x86_64 x86_64 x86_64
== END uname -rmi ==

== BEGIN rpm -qa \*-release\* ==
elrepo-release-6-4.el6.elrepo.noarch
centos-release-6-3.el6.centos.9.x86_64
rpmforge-release-0.5.2-2.el6.rf.x86_64
remi-release-6-1.el6.remi.noarch
epel-release-6-8.noarch
== END rpm -qa \*-release\* ==

== BEGIN cat /etc/redhat-release ==
CentOS release 6.3 (Final)
== END cat /etc/redhat-release ==

== BEGIN getenforce ==
Disabled
== END getenforce ==

== BEGIN free -m ==
total used free shared buffers cached
Mem: 64542 3840 60701 0 319 2218
-/+ buffers/cache: 1302 63240
Swap: 7999 0 7999
== END free -m ==

== BEGIN rpm -qa yum\* rpm-\* python | sort ==
python-2.6.6-29.el6_3.3.x86_64
rpm-build-4.8.0-27.el6.x86_64
rpm-devel-4.8.0-27.el6.x86_64
rpm-libs-4.8.0-27.el6.x86_64
rpm-python-4.8.0-27.el6.x86_64
yum-3.2.29-30.el6.centos.noarch
yum-metadata-parser-1.1.2-16.el6.x86_64
yum-plugin-fastestmirror-1.1.30-14.el6.noarch
yum-utils-1.1.30-14.el6.noarch
== END rpm -qa yum\* rpm-\* python | sort ==

== BEGIN ls /etc/yum.repos.d ==
CentOS-Base.repo
CentOS-Debuginfo.repo
CentOS-Media.repo
CentOS-Vault.repo
elrepo.repo
epel.repo
epel-testing.repo
mirrors-rpmforge
mirrors-rpmforge-extras
mirrors-rpmforge-testing
RCS
remi.repo
rocks-local.repo
rpmforge.repo
== END ls /etc/yum.repos.d ==

== BEGIN cat /etc/yum.conf ==
[main]
cachedir=/var/cache/yum
debuglevel=2
logfile=/var/log/yum.log
pkgpolicy=newest
distroverpkg=redhat-release
tolerant=1
exactarch=1
assumeyes=1

== END cat /etc/yum.conf ==

== BEGIN yum repolist all ==
repo id repo name status
C6.0-base CentOS-6.0 - Base disabled
C6.0-centosplus CentOS-6.0 - CentOSPlus disabled
C6.0-contrib CentOS-6.0 - Contrib disabled
C6.0-extras CentOS-6.0 - Extras disabled
C6.0-updates CentOS-6.0 - Updates disabled
C6.1-base CentOS-6.1 - Base disabled
C6.1-centosplus CentOS-6.1 - CentOSPlus disabled
C6.1-contrib CentOS-6.1 - Contrib disabled
C6.1-extras CentOS-6.1 - Extras disabled
C6.1-updates CentOS-6.1 - Updates disabled
C6.2-base CentOS-6.2 - Base disabled
C6.2-centosplus CentOS-6.2 - CentOSPlus disabled
C6.2-contrib CentOS-6.2 - Contrib disabled
C6.2-extras CentOS-6.2 - Extras disabled
C6.2-updates CentOS-6.2 - Updates disabled
Rocks-6.1 Rocks 6.1 enabled: 2,062
base CentOS-6 - Base disabled
c6-media CentOS-6 - Media disabled
centosplus CentOS-6 - Plus disabled
contrib CentOS-6 - Contrib disabled
debug CentOS-6 - Debuginfo disabled
elrepo ELRepo.org Community Enterprise Linux Repo disabled
elrepo-extras ELRepo.org Community Enterprise Linux Repo disabled
elrepo-kernel ELRepo.org Community Enterprise Linux Kern disabled
elrepo-testing ELRepo.org Community Enterprise Linux Test disabled
epel Extra Packages for Enterprise Linux 6 - x8 enabled: 8,624
epel-debuginfo Extra Packages for Enterprise Linux 6 - x8 enabled: 1,802
epel-source Extra Packages for Enterprise Linux 6 - x8 enabled: 0
epel-testing Extra Packages for Enterprise Linux 6 - Te disabled
epel-testing-debuginfo Extra Packages for Enterprise Linux 6 - Te disabled
epel-testing-source Extra Packages for Enterprise Linux 6 - Te disabled
extras CentOS-6 - Extras disabled
remi Les RPM de remi pour Enterprise Linux 6 - enabled: 992
remi-test Les RPM de remi en test pour Enterprise Li enabled: 153
rpmforge RHEL 6 - RPMforge.net - dag disabled
rpmforge-extras RHEL 6 - RPMforge.net - extras disabled
rpmforge-testing RHEL 6 - RPMforge.net - testing disabled
updates CentOS-6 - Updates disabled
repolist: 13,633
== END yum repolist all ==

== BEGIN egrep 'include|exclude' /etc/yum.repos.d/*.repo ==
== END egrep 'include|exclude' /etc/yum.repos.d/*.repo ==

== BEGIN sed -n -e "/^\[/h; /priority *=/{ G; s/\n/ /; s/ity=/ity = /; p }" /etc/yum.repos.d/*.repo | sort -k3n ==
== END sed -n -e "/^\[/h; /priority *=/{ G; s/\n/ /; s/ity=/ity = /; p }" /etc/yum.repos.d/*.repo | sort -k3n ==

== BEGIN cat /etc/fstab ==

#
# /etc/fstab
# Created by anaconda on Wed Jan 30 18:00:19 2013
#
# Accessible filesystems, by reference, are maintained under '/dev/disk'
# See man pages fstab(5), findfs(8), mount(8) and/or blkid(8) for more info
#
UUID=b2ad4070-bac1-4b13-89b8-cdc9de232604 / ext3 defaults 1 1
UUID=768ee398-6c3f-46d9-8de9-2fe96d9ae654 /boot ext3 defaults 1 2
UUID=6b9a5e37-c298-4113-9ac7-4a45c9991c26 /export ext3 defaults 1 2
UUID=684bed55-8646-4f0d-9115-223cbf686824 /var ext3 defaults 1 2
UUID=3eb1c33e-ca40-4ed2-b518-cdbc2f504667 swap swap defaults 0 0
tmpfs /dev/shm tmpfs defaults 0 0
devpts /dev/pts devpts gid=5,mode=620 0 0
sysfs /sys sysfs defaults 0 0
proc /proc proc defaults 0 0

# The ram-backed filesystem for ganglia RRD graph databases.
tmpfs /var/lib/ganglia/rrds tmpfs size=16522855000,gid=nobody,uid=nobody,defaults 1 0
== END cat /etc/fstab ==

== BEGIN df -h ==
Filesystem Size Used Avail Use% Mounted on
/dev/sda3 49G 5.4G 41G 12% /
tmpfs 32G 24K 32G 1% /dev/shm
/dev/sda1 985M 109M 827M 12% /boot
/dev/sda2 1.1T 13G 974G 2% /export
/dev/sda6 4.9G 943M 3.7G 21% /var
tmpfs 16G 117M 16G 1% /var/lib/ganglia/rrds
== END df -h ==

== BEGIN cat /proc/mdstat ==
Personalities :
unused devices: <none>
== END cat /proc/mdstat ==

== BEGIN rpm -qa kernel\* | sort ==
kernel-2.6.32-279.14.1.el6.x86_64
kernel-devel-2.6.32-279.14.1.el6.x86_64
kernel-doc-2.6.32-279.14.1.el6.noarch
kernel-firmware-2.6.32-279.14.1.el6.noarch
kernel-headers-2.6.32-279.14.1.el6.x86_64
== END rpm -qa kernel\* | sort ==

== BEGIN lspci -nn ==
00:00.0 Host bridge [0600]: Intel Corporation 5520/5500/X58 I/O Hub to ESI Port [8086:3407] (rev 22)
00:01.0 PCI bridge [0604]: Intel Corporation 5520/5500/X58 I/O Hub PCI Express Root Port 1 [8086:3408] (rev 22)
00:02.0 PCI bridge [0604]: Intel Corporation 5520/5500/X58 I/O Hub PCI Express Root Port 2 [8086:3409] (rev 22)
00:03.0 PCI bridge [0604]: Intel Corporation 5520/5500/X58 I/O Hub PCI Express Root Port 3 [8086:340a] (rev 22)
00:04.0 PCI bridge [0604]: Intel Corporation 5520/X58 I/O Hub PCI Express Root Port 4 [8086:340b] (rev 22)
00:05.0 PCI bridge [0604]: Intel Corporation 5520/X58 I/O Hub PCI Express Root Port 5 [8086:340c] (rev 22)
00:06.0 PCI bridge [0604]: Intel Corporation 5520/X58 I/O Hub PCI Express Root Port 6 [8086:340d] (rev 22)
00:07.0 PCI bridge [0604]: Intel Corporation 5520/5500/X58 I/O Hub PCI Express Root Port 7 [8086:340e] (rev 22)
00:08.0 PCI bridge [0604]: Intel Corporation 5520/5500/X58 I/O Hub PCI Express Root Port 8 [8086:340f] (rev 22)
00:09.0 PCI bridge [0604]: Intel Corporation 5520/5500/X58 I/O Hub PCI Express Root Port 9 [8086:3410] (rev 22)
00:0a.0 PCI bridge [0604]: Intel Corporation 5520/5500/X58 I/O Hub PCI Express Root Port 10 [8086:3411] (rev 22)
00:14.0 PIC [0800]: Intel Corporation 5520/5500/X58 I/O Hub System Management Registers [8086:342e] (rev 22)
00:14.1 PIC [0800]: Intel Corporation 5520/5500/X58 I/O Hub GPIO and Scratch Pad Registers [8086:3422] (rev 22)
00:14.2 PIC [0800]: Intel Corporation 5520/5500/X58 I/O Hub Control Status and RAS Registers [8086:3423] (rev 22)
00:1c.0 PCI bridge [0604]: Intel Corporation 82801JI (ICH10 Family) PCI Express Root Port 1 [8086:3a40]
00:1c.4 PCI bridge [0604]: Intel Corporation 82801JI (ICH10 Family) PCI Express Root Port 5 [8086:3a48]
00:1d.0 USB controller [0c03]: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #1 [8086:3a34]
00:1d.1 USB controller [0c03]: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #2 [8086:3a35]
00:1d.2 USB controller [0c03]: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #3 [8086:3a36]
00:1d.3 USB controller [0c03]: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #6 [8086:3a39]
00:1d.7 USB controller [0c03]: Intel Corporation 82801JI (ICH10 Family) USB2 EHCI Controller #1 [8086:3a3a]
00:1e.0 PCI bridge [0604]: Intel Corporation 82801 PCI Bridge [8086:244e] (rev 90)
00:1f.0 ISA bridge [0601]: Intel Corporation 82801JIB (ICH10) LPC Interface Controller [8086:3a18]
00:1f.2 IDE interface [0101]: Intel Corporation 82801JI (ICH10 Family) 4 port SATA IDE Controller #1 [8086:3a20]
01:03.0 VGA compatible controller [0300]: Advanced Micro Devices [AMD] nee ATI ES1000 [1002:515e] (rev 02)
02:00.0 System peripheral [0880]: Hewlett-Packard Company Integrated Lights-Out Standard Slave Instrumentation & System Support [103c:3306] (rev 04)
02:00.2 System peripheral [0880]: Hewlett-Packard Company Integrated Lights-Out Standard Management Processor Support and Messaging [103c:3307] (rev 04)
02:00.4 USB controller [0c03]: Hewlett-Packard Company Integrated Lights-Out Standard Virtual USB Controller [103c:3300] (rev 01)
03:00.0 RAID bus controller [0104]: Hewlett-Packard Company Smart Array G6 controllers [103c:323a] (rev 01)
04:00.0 Ethernet controller [0200]: NetXen Incorporated NX3031 Multifunction 1/10-Gigabit Server Adapter [4040:0100] (rev 42)
04:00.1 Ethernet controller [0200]: NetXen Incorporated NX3031 Multifunction 1/10-Gigabit Server Adapter [4040:0100] (rev 42)
04:00.2 Ethernet controller [0200]: NetXen Incorporated NX3031 Multifunction 1/10-Gigabit Server Adapter [4040:0100] (rev 42)
04:00.3 Ethernet controller [0200]: NetXen Incorporated NX3031 Multifunction 1/10-Gigabit Server Adapter [4040:0100] (rev 42)
== END lspci -nn ==

== BEGIN lsusb ==
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 002 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 003 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 004 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 005 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 006 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 006 Device 002: ID 03f0:7029 Hewlett-Packard
== END lsusb ==

== BEGIN rpm -qa kmod\* kmdl\* ==
== END rpm -qa kmod\* kmdl\* ==

== BEGIN ifconfig -a ==
eth0 Link encap:Ethernet HWaddr E8:39:35:A7:8F:48
inet addr:10.1.1.1 Bcast:10.1.255.255 Mask:255.255.0.0
inet6 addr: fe80::ea39:35ff:fea7:8f48/64 Scope:Link
UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
RX packets:0 errors:0 dropped:0 overruns:0 frame:0
TX packets:261175 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:0
RX bytes:0 (0.0 b) TX bytes:35465374 (33.8 MiB)

eth1 Link encap:Ethernet HWaddr E8:39:35:A7:8F:49
inet addr:164.125.128.143 Bcast:164.125.128.255 Mask:255.255.255.0
inet6 addr: fe80::ea39:35ff:fea7:8f49/64 Scope:Link
UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
RX packets:569284 errors:0 dropped:0 overruns:0 frame:0
TX packets:67180 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:0
RX bytes:142780096 (136.1 MiB) TX bytes:7628764 (7.2 MiB)

lo Link encap:Local Loopback
inet addr:127.0.0.1 Mask:255.0.0.0
inet6 addr: ::1/128 Scope:Host
UP LOOPBACK RUNNING MTU:16436 Metric:1
RX packets:1065072 errors:0 dropped:0 overruns:0 frame:0
TX packets:1065072 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:0
RX bytes:251636237 (239.9 MiB) TX bytes:251636237 (239.9 MiB)

peth0 Link encap:Ethernet HWaddr E8:39:35:A7:8F:48
inet6 addr: fe80::ea39:35ff:fea7:8f48/64 Scope:Link
UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
RX packets:0 errors:0 dropped:0 overruns:0 frame:0
TX packets:261916 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:1000
RX bytes:0 (0.0 b) TX bytes:35529444 (33.8 MiB)
Interrupt:55

peth1 Link encap:Ethernet HWaddr E8:39:35:A7:8F:49
inet6 addr: fe80::ea39:35ff:fea7:8f49/64 Scope:Link
UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
RX packets:682503 errors:0 dropped:0 overruns:0 frame:0
TX packets:71198 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:1000
RX bytes:173766028 (165.7 MiB) TX bytes:7843576 (7.4 MiB)
Interrupt:59

peth2 Link encap:Ethernet HWaddr E8:39:35:A7:8F:4A
BROADCAST MULTICAST MTU:1500 Metric:1
RX packets:0 errors:0 dropped:0 overruns:0 frame:0
TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:1000
RX bytes:0 (0.0 b) TX bytes:0 (0.0 b)
Interrupt:63

peth3 Link encap:Ethernet HWaddr E8:39:35:A7:8F:4B
BROADCAST MULTICAST MTU:1500 Metric:1
RX packets:0 errors:0 dropped:0 overruns:0 frame:0
TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:1000
RX bytes:0 (0.0 b) TX bytes:0 (0.0 b)
Interrupt:67

virbr0 Link encap:Ethernet HWaddr 52:54:00:C0:29:29
inet addr:192.168.122.1 Bcast:192.168.122.255 Mask:255.255.255.0
UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
RX packets:0 errors:0 dropped:0 overruns:0 frame:0
TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:0
RX bytes:0 (0.0 b) TX bytes:0 (0.0 b)

virbr0-nic Link encap:Ethernet HWaddr 52:54:00:C0:29:29
BROADCAST MULTICAST MTU:1500 Metric:1
RX packets:0 errors:0 dropped:0 overruns:0 frame:0
TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:500
RX bytes:0 (0.0 b) TX bytes:0 (0.0 b)

== END ifconfig -a ==

== BEGIN brctl show ==
bridge name bridge id STP enabled interfaces
eth0 8000.e83935a78f48 no peth0
eth1 8000.e83935a78f49 no peth1
virbr0 8000.525400c02929 yes virbr0-nic
== END brctl show ==

== BEGIN route -n ==
Kernel IP routing table
Destination Gateway Genmask Flags Metric Ref Use Iface
255.255.255.255 0.0.0.0 255.255.255.255 UH 0 0 0 eth0
164.125.128.143 10.1.1.1 255.255.255.255 UGH 0 0 0 eth0
164.125.128.0 0.0.0.0 255.255.255.0 U 0 0 0 eth1
192.168.122.0 0.0.0.0 255.255.255.0 U 0 0 0 virbr0
224.0.0.0 0.0.0.0 255.255.255.0 U 0 0 0 eth0
10.1.0.0 0.0.0.0 255.255.0.0 U 0 0 0 eth0
169.254.0.0 0.0.0.0 255.255.0.0 U 1006 0 0 eth0
169.254.0.0 0.0.0.0 255.255.0.0 U 1007 0 0 eth1
0.0.0.0 164.125.128.1 0.0.0.0 UG 0 0 0 eth1
== END route -n ==

== BEGIN sysctl -a | grep .rp_filter ==
error: permission denied on key 'kernel.cad_pid'
error: permission denied on key 'kernel.usermodehelper.bset'
error: permission denied on key 'kernel.usermodehelper.inheritable'
net.ipv4.conf.all.rp_filter = 0
net.ipv4.conf.all.arp_filter = 0
net.ipv4.conf.default.rp_filter = 1
net.ipv4.conf.default.arp_filter = 0
net.ipv4.conf.lo.rp_filter = 1
net.ipv4.conf.lo.arp_filter = 0
net.ipv4.conf.peth0.rp_filter = 1
net.ipv4.conf.peth0.arp_filter = 0
net.ipv4.conf.peth3.rp_filter = 1
net.ipv4.conf.peth3.arp_filter = 0
net.ipv4.conf.peth2.rp_filter = 1
net.ipv4.conf.peth2.arp_filter = 0
net.ipv4.conf.peth1.rp_filter = 1
net.ipv4.conf.peth1.arp_filter = 0
net.ipv4.conf.eth0.rp_filter = 1
net.ipv4.conf.eth0.arp_filter = 0
net.ipv4.conf.eth1.rp_filter = 1
net.ipv4.conf.eth1.arp_filter = 0
net.ipv4.conf.virbr0.rp_filter = 1
net.ipv4.conf.virbr0.arp_filter = 0
net.ipv4.conf.virbr0-nic.rp_filter = 1
net.ipv4.conf.virbr0-nic.arp_filter = 0
== END sysctl -a | grep .rp_filter ==

== BEGIN ip rule show ==
0: from all lookup local
32766: from all lookup main
32767: from all lookup default
== END ip rule show ==

== BEGIN ip route show ==
255.255.255.255 dev eth0 scope link
164.125.128.143 via 10.1.1.1 dev eth0 scope link
164.125.128.0/24 dev eth1 proto kernel scope link src 164.125.128.143
192.168.122.0/24 dev virbr0 proto kernel scope link src 192.168.122.1
224.0.0.0/24 dev eth0 scope link
10.1.0.0/16 dev eth0 proto kernel scope link src 10.1.1.1
169.254.0.0/16 dev eth0 scope link metric 1006
169.254.0.0/16 dev eth1 scope link metric 1007
default via 164.125.128.1 dev eth1
== END ip route show ==

== BEGIN cat /etc/resolv.conf ==
search local cluster
nameserver 127.0.0.1
nameserver 164.125.9.2
== END cat /etc/resolv.conf ==

== BEGIN egrep 'net|hosts' /etc/nsswitch.conf ==
#hosts: db files nisplus nis dns
hosts: files dns
#networks: nisplus [NOTFOUND=return] files
#netmasks: nisplus [NOTFOUND=return] files
netmasks: files
networks: files
netgroup: nisplus
== END egrep 'net|hosts' /etc/nsswitch.conf ==

== BEGIN chkconfig --list | grep -Ei 'network|wpa' ==
NetworkManager 0:off 1:off 2:off 3:off 4:off 5:off 6:off
network 0:off 1:off 2:on 3:on 4:on 5:on 6:off
wpa_supplicant 0:off 1:off 2:off 3:off 4:off 5:off 6:off
== END chkconfig --list | grep -Ei 'network|wpa' ==

[/code]

User avatar
toracat
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Re: installing pymol in centos 6

Post by toracat » 2013/04/22 03:42:08

You have both [i]base[/i] and [i]updates[/i] disabled. that explains why the required packages are not found. You must enable those repositories and try again.

bharat_46010
Posts: 5
Joined: 2013/04/21 02:47:45

Re: installing pymol in centos 6

Post by bharat_46010 » 2013/04/27 13:54:47

Thanks Sir, it worked.

After updating and enabling the repo. , I am getting the following error when I use mpirun. Actually the centos that I am using is installed while installing rocks cluster. Here's the error :

[bme:42039] *** Process received signal ***
[bme:42039] Signal: Segmentation fault (11)
[bme:42039] Signal code: Invalid permissions (2)
[bme:42039] Failing at address: 0x7f093b655340
[bme:42039] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42039] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x2337) [0x7f093c281fa7]
[bme:42039] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96) [0x7f093c2175d6]
[bme:42039] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa) [0x7f093ca47b3a]
[bme:42039] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7) [0x7f093cadc6f7]
[bme:42039] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42039] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42039] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42039] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42039] [ 9] mdrun() [0x405a29]
[bme:42039] *** End of error message ***
Wrote pdb files with previous and current coordinates
[bme:42036] *** Process received signal ***
[bme:42036] Signal: Segmentation fault (11)
[bme:42036] Signal code: Invalid permissions (2)
[bme:42036] Failing at address: 0x7f794bbe3800
[bme:42036] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42036] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x13e2) [0x7f794c4b8052]
[bme:42036] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96) [0x7f794c44e5d6]
[bme:42036] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa) [0x7f794cc7eb3a]
[bme:42036] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7) [0x7f794cd136f7]
[bme:42036] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42036] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42036] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42036] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42036] [ 9] mdrun() [0x405a29]
[bme:42036] *** End of error message ***
[bme:42042] *** Process received signal ***
[bme:42042] Signal: Segmentation fault (11)
[bme:42042] Signal code: Address not mapped (1)
[bme:42042] Failing at address: 0x7f119c3b96b0
[bme:42042] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42042] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1345) [0x7f11972e2fb5]
[bme:42042] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96) [0x7f11972795d6]
[bme:42042] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa) [0x7f1197aa9b3a]
[bme:42042] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7) [0x7f1197b3e6f7]
[bme:42042] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42042] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42042] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42042] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42042] [ 9] mdrun() [0x405a29]
[bme:42042] *** End of error message ***

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