Rosetta3.2.1-Intel-11.

[Anonymous]

Hello Rosetta Developers:

Rosetta: 3.2.1
Compiler: Intel 11.1.072
Python: 2.7
OS: Linux x86_64

Compilation aborts with the following message. Is there a patch available for this one?
Thanks
Ravi

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Compilation output

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./scons.py compiler=icc bin mode=release
scons: Reading SConscript files …
svn: ‘.’ is not a working copy
scons: done reading SConscript files.
scons: Building targets …
icpc -o build/src/release/linux/2.6/64/x86/icc/protocols/Protocol.os -c -Wp64 -wd279 -ip -O3 -Qoption,c,-ip_ninl_max_stats=500 -Qoption,c,-ip_ninl_max_total_stats=5000 -fPIC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/icc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/Protocol.cc
/usr/include/c++/4.4.3/cmath(500): error: identifier “__builtin_fpclassify” is undefined
return __builtin_fpclassify(FP_NAN, FP_INFINITE, FP_NORMAL,
^
detected during:
instantiation of “__gnu_cxx::__enable_if::__value, int>::__type std::fpclassify(_Tp) [with _Tp=float]” at line 176 of “external/boost_1_38_0/boost/functional/hash/detail/hash_float.hpp”
instantiation of “size_t={unsigned long} boost::hash_detail::float_hash_value(T) [with T=float]” at line 304 of “external/boost_1_38_0/boost/functional/hash/hash.hpp”

/usr/include/c++/4.4.3/cmath(500): error: identifier “__builtin_fpclassify” is undefined
return __builtin_fpclassify(FP_NAN, FP_INFINITE, FP_NORMAL,
^
detected during:
instantiation of “__gnu_cxx::__enable_if<_tp>::__value, int>::__type std::fpclassify(_Tp) [with _Tp=double]” at line 176 of “external/boost_1_38_0/boost/functional/hash/detail/hash_float.hpp”
instantiation of “size_t={unsigned long} boost::hash_detail::float_hash_value(T) [with T=double]” at line 309 of “external/boost_1_38_0/boost/functional/hash/hash.hpp”

/usr/include/c++/4.4.3/cmath(500): error: identifier “__builtin_fpclassify” is undefined
return __builtin_fpclassify(FP_NAN, FP_INFINITE, FP_NORMAL,
^
detected during:
instantiation of “__gnu_cxx::__enable_if<_tp>::__value, int>::__type std::fpclassify(_Tp) [with _Tp=long double]” at line 176 of “external/boost_1_38_0/boost/functional/hash/detail/hash_float.hpp”
instantiation of “size_t={unsigned long} boost::hash_detail::float_hash_value(T) [with T=long double]” at line 314 of “external/boost_1_38_0/boost/functional/hash/hash.hpp”

compilation aborted for src/protocols/Protocol.cc (code 2)
scons: *** [build/src/release/linux/2.6/64/x86/icc/protocols/Protocol.os] Error 2
scons: building terminated because of errors.

[Anonymous]

I can’t duplicate it, which makes it hard to fix. Another developer found an issue with icc 11.1 recently; I’ve ask him if it was the same as this error and if so how he fixed it.

You may have noticed that it is failing in the Boost library. Rosetta has not modified Boost, so you may be able to find a solution looking for boost and intel 11.1 errors, rather than looking at rosetta specifically.

[Anonymous]

Hi Developer:

Thanks very much for your reply.
I think this error is due to incorrect include file setting?

Can you please send me your buid flag options. Also what customized changes did you make in your local copy of
rosetta_source/tools/build/*.template files to use intel compilers?

Can you also tell me which file sets the compiler options for ‘os=linux arch=x86 compiler=icc’ combination?
For example,
From where does the compilation gets all these flags (-Wp64 -wd279 etc.)

icpc -o build/src/release/linux/2.6/64/x86/icc/protocols/Protocol.os -c -Wp64 -wd279 -ip -O3 -Qoption,c,-ip_ninl_max_stats=500 -Qoption,c,-ip_ninl_max_total_stats=5000 -fPIC -DNDEBUG -Isrc -Iexternal/include ….

Thanks very much for your time.

Ravi

[Anonymous]

Hello developer:

cxx=icc option doesnt work. It gives me similar error messages.

>I can’t duplicate it, which makes it hard to fix.
Can you please tell me what version of Intel compiler did you use for the duplication.

Can you please ask the developer who had issues with icc 11.1 on whether he has any fix for the problem?

Thanks very much for your time

Ravi

[Anonymous]

On my cluster:

11:12:49 topsail-login1 ~/scr/rosetta_source> python -V
Python 2.4.3
11:13:07 topsail-login1 ~/scr/rosetta_source> icc -V
Intel(R) C Intel(R) 64 Compiler Professional for applications running on Intel(R) 64, Version 11.1 Build 20090827 Package ID: l_cproc_p_11.1.056
Copyright (C) 1985-2009 Intel Corporation. All rights reserved.

11:13:10 topsail-login1 ~/scr/rosetta_source> uname -a
Linux topsail-login1.isis.unc.edu 2.6.18-128.7.1.el5 #1 SMP Wed Aug 19 04:00:49 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

The compile command line:
11:13:13 topsail-login1 ~/scr/rosetta_source> python scons.py -j8 bin mode=release cxx=icc

I copy the file tools/build/site.settings.topsail to tools/build/site.settings. This is for MPI pathing, which is irrelevant here, but I do it out of habit on all topsail compiles.

I don’t think Oliver ever got ICC working on the cluster that was giving him problems. He did post a settings file for that cluster; I have attached it here but it has no ICC flags, so I don’t think it will help. (You would overwrite tools/build/site.settings with this file).

[Anonymous]

The only change I make to use icc is adding “cxx=icc” to the command line. Replacing “compiler=icc” with “cxx=icc” may fix your error (I didn’t spot it before.

You’ve already found tools/build; all the flags that get added are specified somewhere in that mess of files. I don’t know the system very well. Digging around in tools/build/basic.settings may help.

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