Rosetta3.12 installation

[Anonymous]

Hi all,

Here is the long text of my rescent Rosetta installation process. I really appreciate if you can read it and help with the problem!

I am trying to install newest Rosetta3.12 on a cluster I am currently working with (RHEL6). The version of gcc on this cluster is gcc 4.4.7 which means I need to install a newer gcc first.

I don’t have the permission to write the root so that I can’t do “yum install devtoolset-newversion”. I then downloaded gcc 7.5.0 source code under my home directory (/home/nbai/gcc/) and did the configure/build/install with the same path (/home/nbai/gcc).

When I installed this new gcc, I got the error:

error while loading shared libraries: libmpc.so.3: cannot open shared object file: No such file or directory

I noticed this “libmpc.so.3” is not in the /usr/local/lib/ and I need to install it but again, I don’t have permission to write /usr/local/lib. I then installed all these required lib under /home/nbai/gcc again and exported the path in my .bashrc file.

export LD_LIBRARY_PATH=”/home/nbai/gcc/lib/:$LD_LIBRARY_PATH”

I finally installed this new gcc compiler, added the path to bashrc:

export PATH=”/home/nbai/gcc/bin:$PATH”

Now, if I typed:

$gcc –version

I got:

gcc (GCC) 7.5.0

Copyright (C) 2017 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

 

I also tested it with “Hello World” script and it worked.

Finally, I moved to Rosetta compile and when I run:

$ ./scons.py -j8 mode=release bin

I got error:

g++ -o build/src/release/linux/2.6/64/x86/gcc/7.5/default/protocols/init/register4.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7.5 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register4.cc

/home/nbai/gcc/libexec/gcc/x86_64-pc-linux-gnu/7.5.0/cc1plus: error while loading shared libraries: libmpc.so.3: cannot open shared object file: No such file or directory

scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/default/devel/init.os] Error 1

scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/default/apps/public/AbinitioRelax.o] Error 1

scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/default/protocols/init/init.os] Error 1

scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/default/protocols/init/register1.os] Error 1

scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/default/protocols/init/register2.os] Error 1

scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/default/protocols/init/register3.os] Error 1

scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/default/protocols/init/register4.os] Error 1

g++ -o build/src/release/linux/2.6/64/x86/gcc/7.5/default/protocols/antibody_legacy/AntibodyClass.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7.5 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/AntibodyClass.cc

/home/nbai/gcc/libexec/gcc/x86_64-pc-linux-gnu/7.5.0/cc1plus: error while loading shared libraries: libmpc.so.3: cannot open shared object file: No such file or directory

scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/default/protocols/antibody_legacy/AntibodyClass.os] Error 1

scons: building terminated because of errors.

 

It is so werid as this lib “libmpc.so.3” is exactlt the same lib I was missing when installed the gcc and I should fix this problem as gcc was installed successfully.

Could anyone help me with this? Thank you very much! I intsalled Rosetta several times previously, on my Mac and Stampede2, and both times worked smoothly and this is the 1st time I got such a difficult time of Rosetta installation.

Thank you again!

Nan

[Anonymous]

The Rosetta build system sometimes smashes the environment variables. You may be losing the LD_LIBRARY_PATH settings when you’re running under Scons.

I believe in the  source/tools/build/site.settings file, there should be a line like “#            “ENV” : os.environ,” If you uncomment that line (remove the ‘#’ symbol from it), then the full environment (including your LD_LIBRARY_PATH settings) should hopefully be passed through to the compiler.

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