Member Site › Forums › Rosetta 3 › Rosetta 3 – Build/Install › invalid error number in diagnostic control option: 2259
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July 12, 2013 at 10:52 am #1649
Anonymous
Dear rosetta users,
I am trying to install rosetta with mpi. I was able to install without mpi without any errors but with mpi I am getting the following error.scons: Reading SConscript files …
svn_version.py reports this is a non-version-control release version of Rosetta
scons: done reading SConscript files.
scons: Building targets …
mpiCC -o build/src/release/linux/2.6/64/x86/icc/9.1/mpi/protocols/noesy_assign/NoesyModule.os -c -Wp64 -wd279,2259,1682 -ip -O3 -Qoption,c,-ip_ninl_max_stats=500 -Qoption,c,-ip_ninl_max_total_stats=5000 -fPIC -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/icc/9.1 -Isrc/platform/linux/64/icc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/include -I/usr/local/include src/protocols/noesy_assign/NoesyModule.cc
Warning #657: invalid error number in diagnostic control option: 2259src/protocols/noesy_assign/NoesyModule.impl.hh(78): error: identifier “Real” is undefined
Real const min_sym_cont( params.min_contribution_symmetric_peaks_ );
^src/protocols/noesy_assign/NoesyModule.impl.hh(78): error: expected a “;”
Real const min_sym_cont( params.min_contribution_symmetric_peaks_ );
^src/protocols/noesy_assign/NoesyModule.impl.hh(81): error: identifier “min_sym_cont” is undefined
if ( min_sym_cont < 0.99 || ct_repeat == 1 ) {
^compilation aborted for src/protocols/noesy_assign/NoesyModule.cc (code 2)
scons: *** [build/src/release/linux/2.6/64/x86/icc/9.1/mpi/protocols/noesy_assign/NoesyModule.os] Error 2
scons: building terminated because of errors.I am using the command
./scons.py bin mode=release extras=mpi cxx=iccCan someone please help me with this?
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July 12, 2013 at 6:48 pm #9041
I’m take it you’re trying to compile the regular Rosetta3.5 release. (FYI, this is the forum for PyRosetta installation.)
From the error message, it looks like the fix might be to edit src/protocols/noesy_assign/NoesyModule.impl.hh and turn any plain “Real” into “core::Real”
I think there’s more going on, though, as I don’t see why that should be giving you an issue. Are those the only warning/error messages you get? When you compiled without MPI were you also using the icc compiler? Are you on a commercial-off-the-shelf box, or is this a specialized cluster like BlueGene?
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July 13, 2013 at 5:44 am #9045
I am sorry I didn’t realize this was the wrong forum. Yes I am trying to install regular Rosetta 3.5. This is an HCL cluster with infiniband. Yes these are the only warning/error messages I get. I didn’t use icc when I compiled without mpi. But when I compile with mpi without the cxx = icc flag, I get the following error
scons: Building targets …
mpiCC -o build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/apps/public/AbinitioRelax.o -c -std=c++98 -pipe -ffor-scope -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.1 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/include -I/usr/local/include src/apps/public/AbinitioRelax.cc
icpc: Command line error: invalid argument for option ‘-std’
scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/apps/public/AbinitioRelax.o] Error 1
scons: building terminated because of errors.Should I move the question to the appropriate forum or can it be moved by the administrators?
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July 17, 2013 at 1:52 pm #9072
Thanks for the suggestions. The cluster on which I was trying to install rosetta is down since 3-4 days. I will work on your suggestion as soon as the cluster is back up and report back.
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July 18, 2013 at 6:38 am #9080
Hi. The server is back up. I tried installing without mpi with cxx=icc but I got the same errors as I got with mpi (shown in my first post). So it seems I get this error whenever i use cxx=icc. Can you please suggest a way out?
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July 15, 2013 at 7:09 pm #9059
It looks like even without the cxx=icc flag you’re using the icc compiler, but with the flags for gcc – probably because you don’t have a gcc MPI compiler installed.
My suggestion would be to try to compile with icc but without mpi and see how that works. Right now we have two things that might be messing things up, and it might help to find out if it’s the icc that’s not liking things, or is it something with the MPI setup.
Does replacing Real with core::Real in that file help, or are you still getting errors in other files?
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July 18, 2013 at 6:29 pm #9083
I just compiled with icc (non-MPI), and had no issues. (This was the developer version, but the file giving you errors should be the same.) This was with icpc (ICC) version 11.1 20091130
It may be that the particular version of icc you’re using has problems with namespace directives in templated member functions. (From a quick Google search it looks like other people may have had similar problems, but I couldn’t find a definitive bug report.)
As a quick fix, try replacing the plain “Real” with the fully namespaced “core::Real”. There may be several places in the the code where such full namespacing may be required. (So you’ll fix one spot, and then the compiler will complain at another.)
If this doesn’t work, you may need to look into upgrading your icc version. (Assuming you’re using a version older than 11.1.)
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