libmpc.so.2: cannot open shared object file

[Anonymous]

I am attempting to install Rosetta/3.8 on a Linux Cluster running Redhat 5.6. I am compiling with gcc/4.9.3 and mpich 3.2. I have come across the following error:

/exports/apps/gcc/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: error while loading shared libraries: libmpc.so.2: cannot open shared object file: No such file or directory

The issue here I think is that I have two versions of gcc on the server, and the newer version (version 4.9.3) is not installed on a standard path. Additionally, some of the libraries for that compiler, namely libmpc, are also installed on non standard paths. Normally when I compile things with the newer version of gcc I add the path to libmpc and other dependencies to the LD_LIBRARY_PATH environment variable or add the CXXFLAG -L/path/to/libmpc, however, this does not seem to help in this particular situation.

 

Steps I have already taken:

1. I was originally getting an error which stated that mpiCC does not exist so I edited uers.settings and added the line

“CXX” : “mpic++”

2. I was getting an error saying “unrecognized command line option “-std=c++0x””. I attempted to edit basic.settings to change the option to “-std=c++11”, but that had no effect. I have compiled c++11 programs before using gcc/4.9.3 before. After reading this post: https://www.rosettacommons.org/node/9823 I copied site.settings.killdevil to site.settings, resotred basic.settings to its original state from a backup, and the error went away but was replaced with the error I currently have

3. modified users.settings to add the following lines:

“CPPFLAGS” : “-L/exports/apps/gcc/4.9.0-extralibs/lib”

4. Copied and pasted the compilation command I was getting the error from directly into the command line and it compiled with no issue

mpic++ -o build/src/debug/linux/2.6/64/x86/gcc/4.9/mpi/apps/public/AbinitioRelax.o -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DUSEMPI -L/exports/apps/gcc/4.9.0-extralibs/lib -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.9 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include src/apps/public/AbinitioRelax.cc

 

Here is the full output for the error I am getting:

 

scons: Reading SConscript files …

Running versioning script … fatal: Not a git repository (or any parent up to mount parent /exports)

Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

Done. (0.0 seconds)

Number of option files updated: 0

Total 3922 options.

Finished updating ResidueProperty code — no changes needed

Finished updating VariantType code — no changes needed

scons: done reading SConscript files.

scons: Building targets …

mpic++ -o build/src/debug/linux/2.6/64/x86/gcc/4.9/mpi/apps/public/AbinitioRelax.o -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DUSEMPI -L/exports/apps/gcc/4.9.0-extralibs/lib -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.9 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include src/apps/public/AbinitioRelax.cc

/exports/apps/gcc/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: error while loading shared libraries: libmpc.so.2: cannot open shared object file: No such file or directory

scons: *** [build/src/debug/linux/2.6/64/x86/gcc/4.9/mpi/apps/public/AbinitioRelax.o] Error 1

scons: building terminated because of errors.

 

Below is a full listing of my user.settings file:

 

# -*- mode:python;indent-tabs-mode:nil;show-trailing-whitespace:t; -*-

#

# Copy this file into user.settings:

#

#   cp user.settings.template user.settings

#

# and customize to fit your site’s environment

# DO NOT make changes to this template

# DO NOT try and check in user.settings

# (c) Copyright Rosetta Commons Member Institutions.

# (c) This file is part of the Rosetta software suite and is made available under license.

# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.

# (c) For more information, see http://www.rosettacommons.org. Questions about this can be

# (c) addressed to University of Washington CoMotion, email: license@uw.edu.

# Settings here are added to the combined build settings, after all basic

# and site settings, to allow you to override anything you need to.

# They can in turn be overriden by the project settings.

#

# NOTE: At some point this file will allow you to have multiple settings

# and select between them from the options.  For now there is only the

# single “user” settings.

#import os

settings = {

    “user” : {

        “prepends” : {

        },

        “appends” : {

            # Uncomment the line below and the “import os” line above

            # to let SCons find ICC (assuming it’s on your PATH already)

            # This is commented-out by default because it makes SCons

            # sensitive to your entire path.  This is necessary in

            # some environments, but has the unfortunate consequence

            # that any change whatsoever to the PATH variable (or its

            # contents) will force a complete recompile.

            #”program_path”  : os.environ[“PATH”].split(“:”),

            # Uncomment the line below to enable experimental mute level control in Tracer’s

            #”defines” : [ ‘EXPERIMENTAL_TRACER_FEATURES’ ],

            “CPPFLAGS” : “-L/exports/apps/gcc/4.9.0-extralibs/lib”,

#            “CPPFLAGS” : “-L/exports/apps/gcc/4.9.3/lib”,

#            “CPPFLAGS” : “-L/exports/apps/gcc/4.9.3/lib64”

        },

        “overrides” : {

            ## Uncomment the following line to import the full operating system environment.  Useful for

            ## compiling with scons on different systems.

            #”ENV” : os.environ,

            “CXX” : “mpic++”,

            “cc” : “mpicc”,

        },

        “removes” : {

        },

    }

}

Thank you for any help you can provide,

Shane Hesprich

[Anonymous]

Two quick addendums:

First, here is the command I am using to compile:

./scons.py bin build=release extras=mpi

Second, libmpc is installed in the path /exports/apps/gcc/4.9.0-extralibs/lib, and the command ‘ls /exports/apps/gcc/4.9.0-extralibs/lib’ gives the following output:

cmake     libgmp.la  libgmp.so.3      libmpc.a   libmpc.so    libmpc.so.2.0.0  libmpfr.la  libmpfr.so.1      libxml2.a   libxml2.so    libxml2.so.2.9.3  xml2Conf.sh

libgmp.a  libgmp.so  libgmp.so.3.5.2  libmpc.la  libmpc.so.2  libmpfr.a        libmpfr.so  libmpfr.so.1.2.2  libxml2.la  libxml2.so.2  pkgconfig

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