LinuxQuestions.org
Share your knowledge at the LQ Wiki.
Go Back   LinuxQuestions.org > Forums > Linux Forums > Linux - Software
User Name
Password
Linux - Software This forum is for Software issues.
Having a problem installing a new program? Want to know which application is best for the job? Post your question in this forum.

Notices


Reply
  Search this Thread
Old 05-02-2017, 04:50 AM   #1
drrahul
Member
 
Registered: Apr 2017
Posts: 36

Rep: Reputation: Disabled
Gromacs Installation Error


I have installed gcc 5.3 in centOS version 6.9

i am trying to install gromacs 2016.3 and in make check command i am ettin following error.

22% tests passed, 21 tests failed out of 27

Label Time Summary:
GTest = 0.02 sec (18 tests)
IntegrationTest = 0.00 sec (2 tests)
MpiIntegrationTest = 0.00 sec (1 test)
UnitTest = 0.02 sec (18 tests)

Total Test time (real) = 0.82 sec

The following tests FAILED:
1 - TestUtilsUnitTests (Failed)
2 - MdlibUnitTest (Failed)
3 - CommandLineUnitTests (Failed)
4 - FFTUnitTests (Failed)
5 - HardwareUnitTests (Failed)
6 - MathUnitTests (Failed)
7 - OnlineHelpUnitTests (Failed)
8 - OptionsUnitTests (Failed)
9 - RandomUnitTests (Failed)
10 - UtilityUnitTests (Failed)
11 - FileIOTests (Failed)
12 - PullTest (Failed)
13 - SimdUnitTests (Failed)
14 - LegacyToolsTests (Failed)
15 - GmxPreprocessTests (Failed)
16 - CorrelationsTest (Failed)
17 - AnalysisDataUnitTests (Failed)
18 - SelectionUnitTests (Failed)
19 - TrajectoryAnalysisUnitTests (Failed)
20 - MdrunTests (Failed)
21 - MdrunMpiTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest] Error 8
make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
make: *** [check] Error 2


I am advised that I am running in different environment from the one which i have compiled. How do i over come it>?
 
Old 05-02-2017, 07:03 AM   #2
rtmistler
Moderator
 
Registered: Mar 2011
Location: USA
Distribution: MINT Debian, Angstrom, SUSE, Ubuntu, Debian
Posts: 9,353
Blog Entries: 13

Rep: Reputation: 4411Reputation: 4411Reputation: 4411Reputation: 4411Reputation: 4411Reputation: 4411Reputation: 4411Reputation: 4411Reputation: 4411Reputation: 4411Reputation: 4411
How did you install gromacs? You mention compiling it in your last paragraph. Did you compile it on this system where you are running it?

Note that there are instructions how to install it referenced on their web page, http://manual.gromacs.org/documentat...6.3/index.html, and also this type of package usually does require you to build it from source because it is performing a high amount of advanced math computations, therefore it is important to have the software understand the system's capabilities when it gets installed.
 
Old 05-03-2017, 01:34 AM   #3
drrahul
Member
 
Registered: Apr 2017
Posts: 36

Original Poster
Rep: Reputation: Disabled
I am on CentOS 6.9 version loaded with GCC version 5.3.

I use the following commands to install Gromacs

tar xfz gromacs-2016.3.tar.gz
cd gromacs-2016.3
mkdir build
cd build
CC=gcc53 CXX=g++53 cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check

"Here i get errors"

make install


MY GCC details



[root@mqml Desktop]# rpm -qa gcc53-c++
gcc53-c++-5.3.0-1.el6.x86_64

[root@mqml Desktop]# which gcc53
/usr/bin/gcc53

[root@mqml Desktop]# which g++53
/usr/bin/g++53

[root@mqml Desktop]# gcc53 -v
Using built-in specs.
COLLECT_GCC=gcc53
COLLECT_LTO_WRAPPER=/usr/local/gcc53/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-5.3.0/configure --prefix=/usr/local/gcc53 --program-suffix=53 --enable-languages=c,c++ --with-system-zlib --disable-multilib
Thread model: posix
gcc version 5.3.0 (GCC)

[root@mqml Desktop]# g++53 -v
Using built-in specs.
COLLECT_GCC=g++53
COLLECT_LTO_WRAPPER=/usr/local/gcc53/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-5.3.0/configure --prefix=/usr/local/gcc53 --program-suffix=53 --enable-languages=c,c++ --with-system-zlib --disable-multilib
Thread model: posix
gcc version 5.3.0 (GCC)
 
Old 05-03-2017, 01:56 AM   #4
drrahul
Member
 
Registered: Apr 2017
Posts: 36

Original Poster
Rep: Reputation: Disabled
I have installed devtoolset-4.0 and still I receive the same errors. How do I check the present version of devtoolset?

I have followed the following commands to install devtoolset.

sudo yum install centos-release-scl
sudo yum-config-manager --enable rhel-server-rhscl-7-rpms
sudo yum install devtoolset-4
scl enable devtoolset-4 bash
 
  


Reply


Thread Tools Search this Thread
Search this Thread:

Advanced Search

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is Off
HTML code is Off



Similar Threads
Thread Thread Starter Forum Replies Last Post
LXer: Chemistry the Gromacs Way LXer Syndicated Linux News 0 05-22-2012 12:20 AM
About VMWare and Gromacs awmax96 Linux - Newbie 1 09-24-2009 12:51 PM
About VMWare and Gromacs awmax96 Linux - Software 1 09-24-2009 12:44 PM
please guide me with dis.. i am trying to install Gromacs in my system nithinvg Linux - General 11 09-05-2008 10:39 PM

LinuxQuestions.org > Forums > Linux Forums > Linux - Software

All times are GMT -5. The time now is 04:17 PM.

Main Menu
Advertisement
My LQ
Write for LQ
LinuxQuestions.org is looking for people interested in writing Editorials, Articles, Reviews, and more. If you'd like to contribute content, let us know.
Main Menu
Syndicate
RSS1  Latest Threads
RSS1  LQ News
Twitter: @linuxquestions
Open Source Consulting | Domain Registration