installation error

[Anonymous]

Hi, I am building Rosetta3.2 with MPI but it failed, here is the log, can you give me advices? THX

---

log

---

rosetta3.3/rosetta_source> scons bin mode=release extras=mpi
scons: Reading SConscript files …
scons: done reading SConscript files.
scons: Building targets …
mpiCC -o build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbinitioRelax.o -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -I/soft/intel64/icc/ipp/em64t/include -I/soft/intel64/icc/mkl/include -I/soft/intel64/ifort/mkl/include -I/soft/intel64/icc/ipp/em64t/include -I/soft/intel64/icc/mkl/include -I/soft/intel64/ifort/mkl/include -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/apps/public/AbinitioRelax.cc
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbinitioRelax.o] Error 127
scons: building terminated because of errors.

[Anonymous]

sh: mpiCC: command not found

mpiCC is not found. Either you’ve not installed MPI, or SCons can’t see it. Try “which mpiCC” to see if it’s installed; if it is, try fiddling with the SCons paths to fix it. You can overwrite tools/build/site.settings with site.settings.topsail to improve SCons pathing for MPI.

[Anonymous]

A) With ICC, you probably need to use cxx=icc on your compile command line. That alone is likely to fix the problem. “scons bin mode=release extras=mpi cxx=icc -j#” where # is the number of processors available.

I don’t think that settings file is formatted right. First revert site.settings to being empty, then try cxx=icc. If that fails, we (or you) can google for SCons documentation to figure out how to include your explicit paths in that file.

[Anonymous]

I need to compile it with MPI and Infiniband support to run Rosetta on our cluster, but I ran into the same problem.

I made sure that mpiCC (also in my case the mvapich2 cc is named “mpicc” and I had to link it to “mpiCC”) is in path and I can compile other tools with it.

I am not familiar with the scons build system and I could not figure out how to make scons honor the $CC or $MPI_CC system variables or how to force it to use MPICC in a specific path.

Neither mpiCC compiled with GCC or ICC works and the flag “cxx=icc” doesn’t change a thing.

I would be happy for any advice and or hints.

Cheers,
Bjoern

[Anonymous]

Hi Bjoem,

Can you please post the results for the following:

echo $PATH

which mpiCC

cat tools/build/site.settings

On my cluster, I have

> echo $PATH
…:/usr/mpi/gcc/openmpi-1.4.2/bin:…

> which mpiCC
/usr/mpi/gcc/openmpi-1.4.2/bin/mpiCC

and I’ve copies site.settings.topsail to replace site.settings

Also, can you confirm your error message is the same as albumns above?

Best,
Matt

[Anonymous]

Oookay, well, the error was caused by the empty system variable $INCLUDE. Now I can compile rosetta when I copy site.settings.topsail to site.settings
INCLUDE=”${INCLUDE}:/cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/include” did the trick.

No other changes were necessary, except that scons is still looking for mpiCC, but for MVAPICH2 there is no mpiCC as C++ Linker, only mpicxx.
Linking/copying mpicc to mpiCC served me well as a workaround.

Thanks!
Bjoern

[Anonymous]

Okay, just after posting this I ran into another error:

mpiCC -o build/src/release/linux/2.6/64/x86/gcc/mpi/core/conformation/ResidueKinWriter.os -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -I/cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/include -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/core/conformation/ResidueKinWriter.cc
mpicc -o build/external/release/linux/2.6/64/x86/gcc/mpi/libsqlite3.so -shared build/external/release/linux/2.6/64/x86/gcc/mpi/dbio/sqlite3/sqlite3.os -L/cvos/shared/apps/sge/6.2/lib/lx26-amd64 -L/cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/lib/shared -L/usr/local/lib -L/usr/lib -Lexternal/lib
/usr/bin/ld: /cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/lib/libmpich.a(mem_hooks.o): relocation R_X86_64_32 against `a local symbol’ can not be used when making a shared object; recompile with -fPIC
/cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/lib/libmpich.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
scons: *** [build/external/release/linux/2.6/64/x86/gcc/mpi/libsqlite3.so] Error 1
scons: building terminated because of errors.

I’ll giv -fPIC a shot. If someone tells me how to pass compiler flags to scons

Cheers,
Bjoern

[Anonymous]

Sorry my mistake! I accidentally linked mpicc to mpiCC instead of linking mpicxx to mpiCC, also I had to recompile MVAPICH2 with the following flags:
./configure CFLAGS=”-fPIC” CXXFLAGS=”-fPIC” FFLAGS=”-fPIC” (at least when using GCC to compile MVAPICH2)

Cheers,
Bjoern

[Anonymous]

Good job on getting your build configuration working!

Good luck with your predictions and experiments.

Best,
Matt

[Anonymous]

HI,
I am trying to compile the rosetta programs in a mpi mode. I am just trying to follow the things from the forum but not able to build the programs in bin directory. Here is the methods which I am follwing:
gzipped_packages/rosetta_source> ls
Abinitio_MPI.tar.gz lib scons.py
accept_utracers.sh make_ctags.sh SConstruct
analysis performance-benchmark.py src
bin projects.settings stubs
build readme.txt test
external rosetta_database tools
ide SConscript update_options.sh

/gzipped_packages/rosetta_source> ./scons.py bin mode=release extras=static,mpi
scons: Reading SConscript files …
Copy(“user.options”, “user.options.template”)
Copy(“user.settings”, “user.settings.template”)
Copy(“/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/src/pilot_apps.src.settings”, “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/src/pilot_apps.src.settings.template”)
scons: done reading SConscript files.
scons: Building targets …
mpiCC -o build/src/release/linux/2.6/32/x86/gcc/static-mpi/apps/public/AbInitio_MPI.o -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/apps/public/AbInitio_MPI.cc
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/32/x86/gcc/static-mpi/apps/public/AbInitio_MPI.o] Error 127
scons: building terminated because of errors.

Then I checked the mpiCC

which mpiCC
/usr/lib/mpi/gcc/openmpi/bin/mpiCC # I copied the site.settings.topsail file into site.settings and changed the path, which is:import os
settings = {
“site” : {
“prepends” : {
“/usr/lib/mpi/gcc/openmpi/bin/mpiCC” : os.environ[“PATH”].split(“:”),
“include_path” : os.environ[“INCLUDE”].split(“:”),
“library_path” : os.environ[“LD_LIBRARY_PATH”].split(“:”),
},
“appends” : {
},
“overrides” : {
},
“removes” : {
},
},
}

I did so that scons can find the mpicc header file path.

the result of the execution is:
./scons.py bin mode=release extras=static,mpi
scons: Reading SConscript files …
Traceback (most recent call last):
File “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/SConstruct”, line 139, in main
build = SConscript(“tools/build/setup.py”)
File “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py”, line 614, in __call__
return method(*args, **kw)
File “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py”, line 551, in SConscript
return _SConscript(self.fs, *files, **subst_kw)
File “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py”, line 260, in _SConscript
exec _file_ in call_stack[-1].globals
File “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/tools/build/setup.py”, line 411, in
build = setup()
File “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/tools/build/setup.py”, line 403, in setup
build.settings = setup_build_settings(build.options)
File “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/tools/build/setup.py”, line 203, in setup_build_settings
site = Settings.load(“site.settings”, “settings”)
File “/san1/vcp1/people/gaurav/Desktop/gzipped_packages/rosetta_source/tools/build/settings.py”, line 86, in load
execfile(file, settings)
File “site.settings”, line 27, in
File “/usr/lib/python2.6/UserDict.py”, line 22, in __getitem__
raise KeyError(key)
KeyError: ‘INCLUDE’
scons: done reading SConscript files.
scons: Building targets …
scons: `bin’ is up to date.
scons: done building targets.

But there is nothing built in the bin directory!!!!

It seems that I am missing some changes in the site.settings but couldn’t able to properly make that out.
I have to objective to achieve majorily 1. Trying to install whole rosetta with mpi ready applications
2. Have a patch for Abintio_mpi which i want to use for my structure prediction.

Please tell me the orderly solution for achieving my goals. If there is any flags has to be used do let me know the full command for the same.

Thanks

[Anonymous]

After commenting the INCLUDE in site.settings file:
import os
settings = {
“site” : {
“prepends” : {
“/usr/lib/mpi/gcc/openmpi/bin/mpicc” : os.environ[“PATH”].split(“:”),
#”include_path” : os.environ[“INCLUDE”].split(“:”),
“library_path” : os.environ[“LD_LIBRARY_PATH”].split(“:”),
},
“appends” : {
},
“overrides” : {
},
“removes” : {
},
},
}
“site.settings

I tried to compile & the result is as follows

/gzipped_packages/rosetta_source> scons bin mode=release extras=mpi
scons: Reading SConscript files …

scons: done reading SConscript files.
scons: Building targets …
mpiCC -o build/src/release/linux/2.6/32/x86/gcc/mpi/apps/public/AbInitio_MPI.o -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/apps/public/AbInitio_MPI.cc
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/32/x86/gcc/mpi/apps/public/AbInitio_MPI.o] Error 127
scons: building terminated because of errors.

What to do now?

[Anonymous]

Thank you very much. I use Intel ICC for the mpiCC.
I delete site.settings.topsail and edit site.settings as following, but it still doesn’t work:

import os
settings = {
“site” : {
“prepends” : {
“/soft/intel64/icc/bin/intel64/mpiCC” : os.environ[“PATH”].split(“:”),
“/soft/intel64/icc/include” : os.environ[“INCLUDE”].split(“:”),
“/soft/intel64/icc/lib/intel64” : os.environ[“LD_LIBRARY_PATH”].split(“:”),
},
“appends” : {
},
“overrides” : {
},
“removes” : {
},
},
}

[Anonymous]

blub@mrbird $ echo $PATH
/cvos/shared/apps/gcc/4.3.2/bin:/home/blub/.soft/bin:/home/blub/.soft/usr/local/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/sbin:/usr/sbin:/sbin:/usr/sbin:/home/blub/.soft/usr/local/mybin:/home/blub/.soft/usr/local/bin/pdb-tools:.:/cvos/shared/apps/sge/6.2/bin/lx26-amd64:/cvos/local/apps/cluster-tools/bin:/cvos/shared/apps/blub/utils/:/cvos/shared/apps/charmm/c34b2/gcc/single/:/cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/bin:/cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/sbin
19:24:27 [~]
blub@mrbird $ which mpicc
/cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/bin/mpicc
19:24:43 [~]
blub@mrbird $ which mpiCC
/cvos/shared/apps/mvapich2/gcc/64/1.6/r4751/bin/mpiCC

Where mpiCC is a copy of mpicc

About tools/build/site.settings: There is none. Not before and not after running scons
19:31:20 [~/rosetta3.3/rosetta_source]
blub@mrbird $ ls tools/build/
basic.options options.settings setup.py user.options
basic.settings project.settings.template site.options.template user.options.template
doxyfile_constants.py README site.settings.juelich user.settings
doxyfile.py settings.py site.settings.modules user.settings.template
doxygen.py settings.pyc site.settings.scinet utility.py
__init__.py setup_platforms.py site.settings.template utility.pyc
__init__.pyc setup_platforms.pyc site.settings.topsail
19:31:32 [~/rosetta3.3/rosetta_source]
blub@mrbird $

Here’s the exact error:

blub@mrbird $ scons bin mode=release extras=mpi
scons: Reading SConscript files …
Copy(“user.options”, “user.options.template”)
Copy(“user.settings”, “user.settings.template”)
Copy(“/home/blub/rosetta3.3/rosetta_source/src/pilot_apps.src.settings”, “/home/blub/rosetta3.3/rosetta_source/src/pilot_apps.src.settings.template”)
scons: done reading SConscript files.
scons: Building targets …
mpiCC -o build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbinitioRelax.o -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/apps/public/AbinitioRelax.cc
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbinitioRelax.o] Error 127
scons: building terminated because of errors.
19:30:19 [~/rosetta3.3/rosetta_source]

When I simply copy site.settings.topsail to site.settings I get the following error.

19:36:27 [~/rosetta3.3/rosetta_source]
blub@mrbird $ scons bin mode=release extras=mpi
scons: Reading SConscript files …
Copy(“user.options”, “user.options.template”)
Copy(“user.settings”, “user.settings.template”)
Copy(“/home/blub/rosetta3.3/rosetta_source/src/pilot_apps.src.settings”, “/home/blub/rosetta3.3/rosetta_source/src/pilot_apps.src.settings.template”)
Traceback (most recent call last):
File “/home/blub/rosetta3.3/rosetta_source/SConstruct”, line 139, in main
build = SConscript(“tools/build/setup.py”)
File “/usr/lib/scons/SCons/Script/SConscript.py”, line 612, in __call__
return apply(method, args, kw)
File “/usr/lib/scons/SCons/Script/SConscript.py”, line 549, in SConscript
return apply(_SConscript, [self.fs,] + files, subst_kw)
File “/usr/lib/scons/SCons/Script/SConscript.py”, line 259, in _SConscript
exec _file_ in call_stack[-1].globals
File “/home/blub/rosetta3.3/rosetta_source/tools/build/setup.py”, line 411, in ?
build = setup()
File “/home/blub/rosetta3.3/rosetta_source/tools/build/setup.py”, line 403, in setup
build.settings = setup_build_settings(build.options)
File “/home/blub/rosetta3.3/rosetta_source/tools/build/setup.py”, line 203, in setup_build_settings
site = Settings.load(“site.settings”, “settings”)
File “/home/blub/rosetta3.3/rosetta_source/tools/build/settings.py”, line 86, in load
execfile(file, settings)
File “site.settings”, line 23, in ?
File “/usr/lib64/python2.4/UserDict.py”, line 17, in __getitem__
def __getitem__(self, key): return self.data[key]
KeyError: ‘INCLUDE’
scons: done reading SConscript files.
scons: Building targets …
scons: `bin’ is up to date.
scons: done building targets.

Looks like a faulty dictionary… but I have no clue what the dictionarys generated in site.settings have too look like.

Cheers, and thans for your help,
Bjoern

[Anonymous]

It looks like the problem with copying site.settings.topsail is the “include_path” line. If you delete that line and run scons.py, is it able to find mpiCC?

Also hard coding the result of ‘echo $INCLUDE’ into the include path formatted as a python list line like this:

“include_path” : [“/first/path”, “/second/path”]

getting the include_path right will point mpiCC to where to find the system headers that go with the compiler.

Best,
Matt

[Anonymous]

This thread already explains how to fix the KeyError INCLUDE problem. Either create a system variable $INCLUDE (set it to .) or remove the line with INCLUDE from site.settings.

[Anonymous]

Hi,

Can you please let me know hoe to set the variable or path for the include thing as I am trying to build the scons in the mpi. I have changed the site.settings file for mpicc and commented the include as mentioned in of the forum reply.

import os
settings = {
“site” : {
“prepends” : {
“/usr/lib/mpi/gcc/openmpi/bin/mpicc” : os.environ[“PATH”].split(“:”),
#”include_path” : os.environ[“INCLUDE”].split(“:”),
“library_path” : os.environ[“LD_LIBRARY_PATH”].split(“:”),
},
“appends” : {
},
“overrides” : {
},
“removes” : {
},
},
}

The run goes:

/gzipped_packages/rosetta_source> scons bin mode=release extras=mpi
scons: Reading SConscript files …
scons: done reading SConscript files.
scons: Building targets …
mpiCC -o build/src/release/linux/2.6/32/x86/gcc/mpi/apps/public/AbInitio_MPI.o -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/apps/public/AbInitio_MPI.cc
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/32/x86/gcc/mpi/apps/public/AbInitio_MPI.o] Error 127
scons: building terminated because of errors.

Please tell me what,where to edit and how to recompile the file for building??

[Author]

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