Compiling cxx=icc; “icc: command not found”

[Anonymous]

I’m having what I imagine to be a simple to solve problem where I’m just missing something. I am running on RHEL5 and trying to build Rosetta 3.5. I have the Intel Composer compiler v15.0.2. I know that no newer than about 11 is shipped in the config options, but I’ve successfully updated the file before to go so far as 14.0.1. In any case, this appears to be failing well before that would matter. The following occurs when I try to build:

root@newton /opt/sw/packages/rosetta/rosetta-3.5-NEW/rosetta_source (1795) # python2.7 scons.py cxx=icc mode=release
scons: Reading SConscript files …
Copy(“user.options”, “user.options.template”)
Copy(“user.settings”, “user.settings.template”)
Copy(“/opt/sw/packages/rosetta/rosetta-3.5-NEW/rosetta_source/src/pilot_apps.src.settings”, “/opt/sw/packages/rosetta/rosetta-3.5-NEW/rosetta_source/src/pilot_apps.src.settings.template”)
svn_version.py reports this is a non-version-control release version of Rosetta
scons: done reading SConscript files.
scons: Building targets …
icc -o build/external/release/linux/2.6/64/x86/icc/15.0/default/dbio/sqlite3/sqlite3.os -c -wd279,2259,1682 -ip -O3 -Qoption,c,-ip_ninl_max_stats=500 -Qoption,c,-ip_ninl_max_total_stats=5000 -fno-fast-math -fPIC -DNDEBUG -DSQLITE_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/include -I/usr/local/include external/dbio/sqlite3/sqlite3.c
sh: icc: command not found
scons: *** [build/external/release/linux/2.6/64/x86/icc/15.0/default/dbio/sqlite3/sqlite3.os] Error 127
scons: building terminated because of errors.

The compiler is most certainly in the PATH:

root@newton /opt/sw/packages/rosetta/rosetta-3.5-NEW/rosetta_source (1801) # which icc
icc is /opt/intel/composer_xe_2015.2.164/bin/intel64/icc
icc is /opt/intel/composer_xe_2015.2.164/bin/intel64/icc
icc is /opt/intel/composer_xe_2015.2.164/bin/intel64_mic/icc
root@newton /opt/sw/packages/rosetta/rosetta-3.5-NEW/rosetta_source (1802) # echo $PATH
/opt/sw/mpi/mvapich2/2.0.1_intel-15.0.2/bin:/opt/intel/composer_xe_2015.2.164/bin/intel64:/opt/intel/composer_xe_2015.2.164/mpirt/bin/intel64:/opt/intel/composer_xe_2015.2.164/debugger/gdb/intel64_mic/py26/bin:/opt/intel/composer_xe_2015.2.164/debugger/gdb/intel64/py26/bin:/opt/intel/composer_xe_2015.2.164/bin/intel64:/opt/intel/composer_xe_2015.2.164/bin/intel64_mic:/opt/intel/composer_xe_2015.2.164/debugger/gui/intel64:/opt/sw/packages/python/2.7.6/bin:/opt/cluster/packages/dsh-0.25.9/bin:/root/bin:/usr/local/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/X11R6/bin:/opt/cluster/bin:/opt/software/bin:/root/bin
root@newton /opt/sw/packages/rosetta/rosetta-3.5-NEW/rosetta_source (1803) # icc -V
Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 15.0.2.164 Build 20150121
Copyright (C) 1985-2015 Intel Corporation. All rights reserved.

This is coming from a fresh extraction of the rosetta3.5_bundles.tgz file.

Thanks in advance for any advice.

[Anonymous]

There’s an issue with the scons build system that it doesn’t necessarily recognize the external path – you have to enable it manually.

Open rosetta_source/tools/build/user.settings with a text editor and uncomment (remove the “#” from the front of) the lines “import os” and “”program_path” : os.environ[“PATH”].split(“:”),”

[Anonymous]

Sure enough — my last build had those things uncommented and I didn’t notice the difference. Thanks for your quick response!

[Author]

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