I am trying to install the ab-initio program quantum-espresso (v. 7) on my centos 7.9 system. The different sub-programs compile and link without error. While the main programs work fine (command line/file based), the gui (PWgui) raises an error when it run stating that "itk" (object-oriented extensions to Tk) is not installed. It is, however installed (take a look at the clipping below for reference). Any suggestions as to how to resolve this?
(base) > /data/Software/qe-7.0/GUI/PWgui>./pwgui
==================================================
This is PWgui version: 7.0
--------------------------------------------------
PWgui: using the system default "tclsh" interpreter
PWGUI : /data/Software/qe-7.0/GUI/PWgui
GUIB engine : /data/Software/qe-7.0/GUI/PWgui/lib/Guib-0.6
can't find package itk
while executing
"package require itk"
(file "/data/Software/qe-7.0/GUI/PWgui/lib/Guib-0.6/init.tcl" line 12)
invoked from within
"source /data/Software/qe-7.0/GUI/PWgui/lib/Guib-0.6/init.tcl"
("package ifneeded Guib 0.6" script)
invoked from within
"package require Guib 0.5"
(file "/data/Software/qe-7.0/GUI/PWgui/init.tcl" line 5)
invoked from within
"source [file join $env(PWGUI) init.tcl]"
(file "/data/Software/qe-7.0/GUI/PWgui/pwgui.tcl" line 60)
(base) > su
Password:
(base) > :/data/Software/qe-7.0/GUI/PWgui>yum install itk-devel
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
* base: ftp.iij.ad.jp
* centos-sclo-rh: ftp.iij.ad.jp
* centos-sclo-sclo: ftp.iij.ad.jp
* epel: ftp.iij.ad.jp
* extras: ftp.iij.ad.jp
* updates: ftp.iij.ad.jp
Package itk-devel-3.4-9.el7.x86_64 already installed and latest version
Nothing to do
Current stable version of ITK is 5.2.1. ITK 3.4 is 15 years old. I think Tk could access ITK in some old versions. But this smells like versions problem.
Related
When trying to run a program in python from the terminal I get the following error:
Fatal Python error: Py_Initialize: unable to load the file system codec
LookupError: no codec search functions registered: can't find encoding
Current thread 0x00007fffb68a93c0 (most recent call first):
Abort trap: 6
I am currently running Python 3.6.4 :: Anaconda custom (64-bit) and think this problem may have to do with also having Anaconda 2 installed. Could someone help me figure out what the cause is and how I can remedy this?
I'd also be interested in knowing more tips about how to use Anaconda 2 and 3 concurrently so that this doesn't happen again.
After some trouble shooting w/ you, it looks like reinstalling anaconda (from the version 3.6 choice on the web) crossed some wires.
For others either...
1) Use your original installment and make a python3 environment. To do this change your .bash_profile to only include
export PATH="/Users/<username>/anaconda2/bin:$PATH
and perhaps remove or move the
/Users/<username>/anaconda3
directory to a new name. Then make a new environment using the original anaconda(with python version 2) that fetches and uses Python 3.6:
conda create -n mypython3environment python=3.6
where "mypython3environment" is some name you want when you use python 3.6
then to use it in your project - go to your project's directory and type:
source activate mypython3environment
2) Do a clean install. The other option is to cut out the anaconda stuff from your .bash_profile, remove or move the anaconda2/ and anaconda3 directories and the .bash_profile.pysave file and try to reinstall from the anaconda webpage.
Overall - you need to install anaconda once - then use conda create and source activate <environment name> to make then use environments, respectively, with your Python version of choice, whether it is a Python 2 or 3 version.
See Anaconda's Managing Environments and the cheatsheet
Running command
sudo yum install php56w-imap
gives me the output:
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
* base: mirrors.163.com
* extras: mirrors.163.com
* updates: mirrors.163.com
* webtatic: uk.repo.webtatic.com
Resolving Dependencies
--> Running transaction check
---> Package php56w-imap.x86_64 0:5.6.22-1.w7 will be installed
--> Processing Dependency: libc-client.so.2007()(64bit) for package: php56w-imap-5.6.22-1.w7.x86_64
--> Finished Dependency Resolution
Error: Package: php56w-imap-5.6.22-1.w7.x86_64 (webtatic)
**Requires: libc-client.so.2007()(64bit)**
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
I'm avoiding any compilation, so the --libdir=/usr/lib64 option for compiling php is not what I'm looking for.
Also, I couldn't find any valid download link for this library.
Please help!
I found it:
https://www.rpmfind.net/linux/rpm2html/search.php?query=libc-client.so.2007()(64bit)
What I tried to install is libc-client-devel but it failed for dependency. with this libc-client, everything works well
just install first with command:
yum install php-imap*
I was getting an SE_UID not found error.
I just stumbled on https://centos.pkgs.org/7/ius-x86_64/php72u-imap-7.2.17-1.ius.centos7.x86_64.rpm.html
and then I ran:
yum install php72u-imap
I also created a php file with echo phpinfo() and saw that IMAP now shows up as a separate section in the display.
OS: CentOS 7
GDB-7.11
I need GDB-7.11 because there is finally support for thread names to appear in the debugger on a remote debug session. I can not get the thread names to show up, however and I believe it is because when I run GDB I am getting the following:
warning: Can not parse XML target description; XML support was disabled at compile time
if i use: yum whatprovides libexpat
[root#localhost lib64]# yum whatprovides libexpat
Loaded plugins: auto-update-debuginfo, fastestmirror, langpacks, nvidia
Loading mirror speeds from cached hostfile
* base: mirror.fdcservers.net
* elrepo: ord.mirror.rackspace.com
* epel: mirror.steadfast.net
* epel-debuginfo: mirror.steadfast.net
* extras: chicago.gaminghost.co
* ius: ord.mirror.rackspace.com
* ius-debuginfo: ord.mirror.rackspace.com
* updates: mirror.sesp.northwestern.edu
expat-2.1.0-8.el7.i686 : An XML parser library
Repo : base
Matched from:
Provides : libexpat.so.1
it is clearly there, located in /usr/lib64
when i run ./configure --with-read-line --with-libexpat
.
.
.
checking whether to use expat... auto
checking for libexpat... (cached) no
configure: WARNING: expat is missing or unusable; some features may be unavailable.
.
.
.
so again, the question is, why can GDB's configure script not find it; it seems to find everything else...?
yum install expat-devel
(copied from #ks1322 comment)
The original error I observed was
checking for libexpat... no
configure: error: expat is missing or unusable
gmake[1]: *** [configure-gdb] Error 1
This error is strange because yum install expat installs shared library file /usr/lib64/libexpat.so.1.
The yum install expat-devel installs shared library file /usr/lib64/libexpat.so. It appears GNU configure only searches for libexpat.so.
The version of gdb 8.3 has the same problem.
I thought of various ways, but I still can't work.
In the end, I used the 10.2 version and all the problems were gone.
I would appreciate if anyone could guide me towards a solution/understanding for the following error message :
f = h5py.File(filename, 'w', driver='mpio', comm=comm)
File "/usr/lib/python2.7/dist-packages/h5py/_hl/files.py", line 149, in __init__
fapl = make_fapl(driver,libver,**kwds)
File "/usr/lib/python2.7/dist-packages/h5py/_hl/files.py", line 37, in make_fapl
raise ValueError('Unknown driver type "%s"' % driver)
ValueError: Unknown driver type "mpio"
I installed h5py using the ubuntu software center. (I ran h5cc -showconfig and noted that parallel HDF5 was enabled.)
I am running on a macbook air with core 2 duo, with only one core enabled for a virtual desktop of ubuntu 13.04.
The version of h5py that comes with Ubuntu was not built against parallel HDF5. That's why you can't use the MPI driver. You need to build h5py by hand. The most convenient way is to use a virtualenv environment, so that the parallel h5py version does not interfere with the Ubuntu-installed version. All you have to do is:
Unpack the h5py source code from h5py.org
Make sure you are in a virtualenv (or don't, if you prefer to install h5py globally. But then you better uninstall h5py in Ubuntu)
$ export CC=mpicc
$ python setup.py build --mpi
$ python setup.py install
That's it. See http://docs.h5py.org/en/latest/mpi.html for details.
I'm new to Macs (and quite new to Django) and I'm setting up an existing Django/MySQL site that uses Mercurial as a site package, on a new Macbook Pro.
All was going well during installation - no error messages. I installed the default versions of most packages from macports.
However when I try runserver, localhost shows the following error message:
ImportError at /
.../lib/python2.6/site-packages/mercurial/osutil.so: no appropriate 64-bit architecture (see "man python" for running in 32-bit mode)
Please could anyone advise? I've tried typing the following at the terminal:
defaults write com.apple.versioner.python Prefer-32-Bit -bool yes
but it didn't help.
I've gotten a similar error and a combination of two things helped me install Mercurial for OS X Lion. I'm running OS X 10.7.3.
First, there is a bug on line 455 of the setup.py script (at least for Mercurial 2.2.1, the version I tried). The line
version = runcmd(['/usr/bin/xcodebuild', '-version'], {})[0].splitlines()
should be replaced with
version = runcmd(['/usr/bin/xcodebuild', '-version'], {})[0]
Second, after I installed Mercurial (either by easy_install, Mac OS X binary installer, and compilation), I kept getting the following error message:
ImportError: dlopen(/Library/Python/2.7/site-packages/mercurial/osutil.so, 2): no suitable image found. Did find: /Library/Python/2.7/site-packages/mercurial/osutil.so: mach-o, but wrong architecture
However, after seeing this post, I noticed that
defaults read com.apple.versioner.python Prefer-32-Bit
outputs 1 on my system. However, running this command
defaults write com.apple.versioner.python Prefer-32-Bit -bool no
and then recompiling / installing mercurial resulted in a working executable for me at the end.
If everything from my comment checks out, try setting that Prefer-32-bit in an user environment variable instead of at the command line.
Edit this file: ~/.MacOSX/environment.plist
See:
http://developer.apple.com/mac/library/documentation/MacOSX/Conceptual/BPRuntimeConfig/Articles/EnvironmentVars.html#//apple_ref/doc/uid/20002093-113982