Compiler C++11

drrahul · 04-17-2017, 07:00 AM

I am trying to install GROMACS on my workstation (centOS 6.3)

[root@mqml build]# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
CMake Error at cmake/gmxTestCXX11.cmake:113 (message):
This version of GROMACS requires a C++11 compiler. Please use a newer
compiler or use the GROMACS 5.1.x release. See the installation guide for
details.
Call Stack (most recent call first):
CMakeLists.txt:164 (gmx_test_cxx11)

-- Configuring incomplete, errors occurred!
See also "/gromacs-2016.1/CMakeFiles/CMakeOutput.log".
See also "/gromacs-2016.1/CMakeFiles/CMakeError.log".
[root@mqml build]# how do I install C++11 ?

jpollard · 04-17-2017, 08:48 AM

I think you will need to update your CentOS to get the newer compiler.

You can try using/setting the compile option to "-std=c11", but you better check that your version supports the standard.

If I do a "gcc -std=c11" (with no source), I get an error about their being no source, but if I use some random string instead of "c11" I get a "unrecognized command line option..." instead.

That should let you find out if c11 is supported by your current compiler.

knudfl · 04-17-2017, 11:23 AM

There are extra later compilers avilable for CentOS 6 : 'devtoolset-4'.
But they use the system gcc-4.4.7 libs :
{/lib64/libgcc*, /usr/lib64/libstdc++*}, i.e. no C++11 support.

You can use "gcc53-c++-5.3.0-1.el6.x86_64.rpm" : Has internal libs ...
/ / /gcc53/lib64/{libgcc_s.so.1, libstdc++.so.6 -> libstdc++.so.6.0.21}
Download link https://drive.google.com/file/d/0B7S...ew?usp=sharing
Provides /usr/bin/{gcc53, g++53} → → $ CC=gcc53 CXX=g++53 cmake ..

By the way, I got no C++11 text when testing gromacs-5.1.4 with gcc-4.4.7 :

Code:

cd build/ && cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
.
.
-- gcc 4.4.7 detected, using -O3, will apply workaround for optimization bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
. 
.

drrahul · 04-17-2017, 01:23 PM

Quote:

Originally Posted by jpollard

I think you will need to update your CentOS to get the newer compiler.

You can try using/setting the compile option to "-std=c11", but you better check that your version supports the standard.

If I do a "gcc -std=c11" (with no source), I get an error about their being no source, but if I use some random string instead of "c11" I get a "unrecognized command line option..." instead.

That should let you find out if c11 is supported by your current compiler.

Can you give me the full command?

drrahul · 04-17-2017, 01:24 PM

Quote:

Originally Posted by knudfl

There are extra later compilers avilable for CentOS 6 : 'devtoolset-4'.
But they use the system gcc-4.4.7 libs :
{/lib64/libgcc*, /usr/lib64/libstdc++*}, i.e. no C++11 support.

You can use "gcc53-c++-5.3.0-1.el6.x86_64.rpm" : Has internal libs ...
/ / /gcc53/lib64/{libgcc_s.so.1, libstdc++.so.6 -> libstdc++.so.6.0.21}
Download link https://drive.google.com/file/d/0B7S...ew?usp=sharing
Provides /usr/bin/{gcc53, g++53} → → $ CC=gcc53 CXX=g++53 cmake ..

By the way, I got no C++11 text when testing gromacs-5.1.4 with gcc-4.4.7 :

Code:

cd build/ && cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
.
.
-- gcc 4.4.7 detected, using -O3, will apply workaround for optimization bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
. 
.

It is only for versions above 2016.1. How to upgrade to devtoolset 4.0?
Can I have the command?

knudfl · 04-17-2017, 03:32 PM

Re #5.

All "devtoolsets" are using old files = {/lib64/libgcc*, /usr/lib64/libstdc++*}.

No C++11 support.

The 'gcc53-c++-5.3.0-1.el6.x86_64.rpm' (48.7MB) was built here, 'July 2016'.
Works very well with gromacs-2016.3 :

Code:

-- The C compiler identification is GNU 5.3.0
-- The CXX compiler identification is GNU 5.3.0
-- Check for working C compiler: /usr/bin/gcc53
-- Check for working C compiler: /usr/bin/gcc53 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++53
-- Check for working CXX compiler: /usr/bin/g++53 -- works
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT - Success

drrahul · 04-18-2017, 04:51 AM

Quote:

Originally Posted by knudfl

Re #5.

All "devtoolsets" are using old files = {/lib64/libgcc*, /usr/lib64/libstdc++*}.

No C++11 support.

The 'gcc53-c++-5.3.0-1.el6.x86_64.rpm' (48.7MB) was built here, 'July 2016'.
Works very well with gromacs-2016.3 :

Code:

-- The C compiler identification is GNU 5.3.0
-- The CXX compiler identification is GNU 5.3.0
-- Check for working C compiler: /usr/bin/gcc53
-- Check for working C compiler: /usr/bin/gcc53 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++53
-- Check for working CXX compiler: /usr/bin/g++53 -- works
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT - Success

Can you please explain in detail about installing the package?

knudfl · 04-18-2017, 05:16 AM

Re #7.

@drrahul, please do not quote entire posts. A "one word reference" will do.

Installing a package downloaded to Downloads/ :

Code:

cd Downloads/
# yum install ./gcc53-c++-5.3.0-1.el6.x86_64.rpm

drrahul · 04-18-2017, 05:37 AM

Quote:

Originally Posted by knudfl

Re #7.

getting the folowing error.

[root@mqml Downloads]# yum install ./gcc53-c++-5.3.0-1.el6.x86_64.rpm
Loaded plugins: aliases, changelog, fastestmirror, kabi, presto, refresh-
: packagekit, security, tmprepo, verify, versionlock
Loading support for CentOS kernel ABI
Setting up Install Process
Examining ./gcc53-c++-5.3.0-1.el6.x86_64.rpm: gcc53-c++-5.3.0-1.el6.x86_64
./gcc53-c++-5.3.0-1.el6.x86_64.rpm: does not update installed package.
Error: Nothing to do

knudfl · 04-18-2017, 10:45 AM

Re #9.

Which other package by name 'gcc53-c++' could be present ? May be you already had installed it ?

Please check with : rpm -qa | grep gcc53

-