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Old 11-26-2014, 03:15 AM   #1
Sonia Bargn
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installing GMT(generic mapping tools) in Centos6


hi everybody!
I wish everything be ok,safe and sound for all of you!
I want to install GMT in Centos6, since it is not in software so I install epel_release(extra pakages) and then install gmt by "yum install".but when I enter a command of GMT in command tool (like psxy) there is and error :

psxy: error while loading shared libraries: libhdf5_hl.so.6: cannot open shared object file: No such file or directory

I have installed it's RPM from
http://rpmfind.net/linux/rpm2html/se...y=libhdf5.so.6

but the problem isn't solved...

what shall I do now? I'm so confusing. thanks for your attention .

Last edited by Sonia Bargn; 11-26-2014 at 05:06 AM.
 
Old 11-26-2014, 04:35 AM   #2
knudfl
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CentOS 6 : # yum install GMT-devel

GMT is in the EPEL.repo https://fedoraproject.org/wiki/EPEL

Available packages :
GMT - Generic Mapping Tools
GMT-coastlines - Coastline data for GMT
GMT-coastlines-full - Full resolution coastline data for GMT
GMT-coastlines-high - High resolution coastline data for GMT
GMT-common - Common files for GMT
GMT-devel - Development files for GMT
GMT-doc - Documentation for GMT
GMT-octave - Octave libraries for GMT
GMT-static - Static libraries for GMT

-
 
Old 11-26-2014, 04:41 AM   #3
knudfl
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*
libhdf5_hl.so.6 is provided by the package 'hdf5' :
# yum install hdf5


Please try $ yum provides */libhdf5_hl.so.6
 
Old 11-26-2014, 05:14 AM   #4
Sonia Bargn
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Quote:
Originally Posted by knudfl View Post
CentOS 6 : # yum install GMT-devel

GMT is in the EPEL.repo https://fedoraproject.org/wiki/EPEL

Available packages :
GMT - Generic Mapping Tools
GMT-coastlines - Coastline data for GMT
GMT-coastlines-full - Full resolution coastline data for GMT
GMT-coastlines-high - High resolution coastline data for GMT
GMT-common - Common files for GMT
GMT-devel - Development files for GMT
GMT-doc - Documentation for GMT
GMT-octave - Octave libraries for GMT
GMT-static - Static libraries for GMT

-


thank you,
I did it but i see this error : psxy: error while loading shared libraries: libhdf5_hl.so.6: cannot open shared object file: No such file or directory

what's your idea about it?
 
Old 11-26-2014, 05:28 AM   #5
Sonia Bargn
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Quote:
Originally Posted by knudfl View Post
*
libhdf5_hl.so.6 is provided by the package 'hdf5' :
# yum install hdf5


Please try $ yum provides */libhdf5_hl.so.6
thanks for your reply,
I've installed hdf5-openmpi-1.8.5.patch1-9.el6.x86_64
to tell the truth i can't find a package which named "libhdf5'
what's your idea?
 
Old 11-26-2014, 05:47 AM   #6
knudfl
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← #5 .
Quote:
I can't find a package which named "libhdf5'
? What do you mean ? The package name is `hdf5´.

Redhat, Fedora, CentOS ...
don't necessarily use lib* for a package with libraries.
"hdf5" provides /usr/lib(64)/libhdf5_hl.so.6 ->
/usr/lib(64)/libhdf5_hl.so.6.0.4 , etc. etc. :
$ rpm -ql hdf5


-

Last edited by knudfl; 11-26-2014 at 05:49 AM.
 
Old 11-26-2014, 06:29 AM   #7
Sonia Bargn
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Quote:
Originally Posted by knudfl View Post
← #5 .

? What do you mean ? The package name is `hdf5´.

Redhat, Fedora, CentOS ...
don't necessarily use lib* for a package with libraries.
"hdf5" provides /usr/lib(64)/libhdf5_hl.so.6 ->
/usr/lib(64)/libhdf5_hl.so.6.0.4 , etc. etc. :
$ rpm -ql hdf5


-
when I enter rpm -ql hdf5 in command tool the output is
[root@sonia Downloads]# rpm -ql hdf5
/usr/bin/gif2h5
/usr/bin/h52gif
/usr/bin/h5c++
/usr/bin/h5cc
/usr/bin/h5copy
/usr/bin/h5debug
/usr/bin/h5diff
/usr/bin/h5dump
/usr/bin/h5fc
/usr/bin/h5import
/usr/bin/h5jam
/usr/bin/h5ls
/usr/bin/h5mkgrp
/usr/bin/h5perf_serial
/usr/bin/h5redeploy
/usr/bin/h5repack
/usr/bin/h5repart
/usr/bin/h5stat
/usr/bin/h5unjam
/usr/lib64/libhdf5.so.7
/usr/lib64/libhdf5.so.7.0.1
/usr/lib64/libhdf5_cpp.so.7
/usr/lib64/libhdf5_cpp.so.7.0.1
/usr/lib64/libhdf5_fortran.so.7
/usr/lib64/libhdf5_fortran.so.7.0.1
/usr/lib64/libhdf5_hl.so.7
/usr/lib64/libhdf5_hl.so.7.0.1
/usr/lib64/libhdf5_hl_cpp.so.7
/usr/lib64/libhdf5_hl_cpp.so.7.0.1
/usr/lib64/libhdf5hl_fortran.so.7
/usr/lib64/libhdf5hl_fortran.so.7.0.1
/usr/share/doc/hdf5-1.8.7
/usr/share/doc/hdf5-1.8.7/CMake.txt
/usr/share/doc/hdf5-1.8.7/CMakeLists.txt
/usr/share/doc/hdf5-1.8.7/COPYING
/usr/share/doc/hdf5-1.8.7/HISTORY-1_0-1_8_0_rc3.txt
/usr/share/doc/hdf5-1.8.7/HISTORY-1_8.txt
/usr/share/doc/hdf5-1.8.7/INSTALL
/usr/share/doc/hdf5-1.8.7/INSTALL_Cygwin.txt
/usr/share/doc/hdf5-1.8.7/INSTALL_MinGW.txt
/usr/share/doc/hdf5-1.8.7/INSTALL_VMS.txt
/usr/share/doc/hdf5-1.8.7/INSTALL_Windows.txt
/usr/share/doc/hdf5-1.8.7/INSTALL_Windows_From_Command_Line.txt
/usr/share/doc/hdf5-1.8.7/INSTALL_Windows_Short_NET.TXT
/usr/share/doc/hdf5-1.8.7/INSTALL_Windows_Short_VS2005.TXT
/usr/share/doc/hdf5-1.8.7/INSTALL_Windows_Short_VS2008.TXT
/usr/share/doc/hdf5-1.8.7/INSTALL_parallel
/usr/share/doc/hdf5-1.8.7/README.txt
/usr/share/doc/hdf5-1.8.7/RELEASE.txt
/usr/share/doc/hdf5-1.8.7/USING_Windows.txt

unfortunetly there is no number 6 of it (I mean in libhdf5_hl.so.6)
 
Old 11-26-2014, 06:39 AM   #8
Sonia Bargn
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Quote:
Originally Posted by knudfl View Post
← #5 .

? What do you mean ? The package name is `hdf5´.

Redhat, Fedora, CentOS ...
don't necessarily use lib* for a package with libraries.
"hdf5" provides /usr/lib(64)/libhdf5_hl.so.6 ->
/usr/lib(64)/libhdf5_hl.so.6.0.4 , etc. etc. :
$ rpm -ql hdf5


-
Dear knudfl
when I enter yum install hdf5 I face this:

[root@sonia Downloads]# yum install hdf5
Loaded plugins: fastestmirror, refresh-packagekit
Setting up Install Process
Loading mirror speeds from cached hostfile
* base: ftp.ntua.gr
* epel: epel.mirror.srv.co.ge
* extras: ftp.ntua.gr
* rpmforge: mirror.ate.info
* updates: ftp.ntua.gr
Package hdf5-1.8.7-1.el6.rf.x86_64 already installed and latest version
Nothing to do

but when I try to use GMT I see the error again

[sonia@sonia Downloads]$ psxy
psxy: error while loading shared libraries: libhdf5_hl.so.6: cannot open shared object file: No such file or directory

what's your idea about this problem?
 
Old 11-26-2014, 07:57 AM   #9
knudfl
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← #7 : Please do not quote entire posts.
A "one word reference" will do.
And no need to show the hdf5 file list. We all know that.


← #8 .
Quote:
Package hdf5-1.8.7-1.el6.rf.x86_64 already installed ...
rf means a repoforge / rpmforge package.
The repoforge.repo is not compatible with the original CentOS repo´s.
Can be used temporary for a single application.
But usually not for system libraries.
And never for a "yum update".

You can type # yum install <package> --disablerepo=repoforge
... or use "Yum priority".
The easy way : $ cd /etc/yum.repos.d/
# mkdir backup
# mv repoforge.repo backup/
... That saves you from remembering the long commands to "disable".


$ psxy
No issues with a default CentOS 6 - x86_64 :
Tested OK a few minutes ago.

-

Last edited by knudfl; 11-26-2014 at 07:59 AM.
 
Old 11-26-2014, 08:25 AM   #10
Sonia Bargn
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Dear all,
I just found the solution
it's because of rpm:
first off all I did this:
cd /etc/yum.repos.d/
I just keep these :
CentOS-Base.repo CentOS-Media.repo
CentOS-Debuginfo.repo CentOS-Vault.repo
CentOS-fasttrack.repo

and then deleted others.(it's importatnt do keep JUST CENTOS REPO at this step)

second: I updated Cent by yum update
third: I restarted Cent
forth: yum remove GMT
yum remove epel-release (if it exit)
fifth : it's important to delet all of hdf5* library that I installed befor
so I did this : yum remove hdf5*


after all I installed epel again : yum install epel-release
then I installed GMT : yum install GMT

it's amazing friend!!
now GMT works in my operating system.
I'm so happy because I was not able to do my thesis for about 2 weeks and I was disappointed but now I did it
don't lose your hope , there is no " it's not possible "
try more and more and be hopeful for your problem
 
Old 11-26-2014, 12:42 PM   #11
Sonia Bargn
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Thanks for you reply.
well... why do we need make a seprate directory for repoforge.repo ?
 
Old 11-26-2014, 01:37 PM   #12
knudfl
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← #11 .
Quote:
why do we need make a seprate directory for repoforge.repo ?
Please read post #9 carefully.
Moving away (saving) the repoforge.repo to <any-folder>/
.. is only to make sure that you aren't using the repo by mistake.
( You can as well just delete the repoforge.repo ).
And : repoforge.repo is for temporary use only.
But you can also use "yum priority",
.. and set the repoforge.repo to the lowest priority.


-

Last edited by knudfl; 11-26-2014 at 01:41 PM.
 
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