Error MPI build rosetta2014.35 on Ubuntu14.04 LTS

[Anonymous]

Hello!

Recently, I posted some post about install Rosetta3.5 on cygwin.

Finally, I changed the OS and succeeded to install them on the Ubuntu on Virtual box(Win7)
Normal install was good. and docking protocol was worked(I only checked that exe).
./scons.py -j4 mode=release bin

But,I couldn’t MPI install by follow command in another new Virtual machine. The first one hour from the beginning was good but I got some error.
I did all command as superuser

sudo apt-get install openmpi-bin
sudo su
./scons.py -j4 mode=release bin extras=mpi

mpiCC -o build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/libutility.so -Wl,-rpath=/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/build/external/release/linux/3.13/64/x86/gcc/4.8/mpi -Wl,-rpath=$ORIGIN -Wl,-rpath=$ORIGIN/../lib -shared build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/libsvm/Svm_rosetta.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/libsvm/Svm.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/tag/Tag.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/lua/LuaIterator.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/lua/LuaObject.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/pointer/ReferenceCount.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/pointer/ReferenceCountMI_.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/options/keys/OptionKeys.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/excn/Exceptions.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/thread/ReadWriteMutex.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/json_spirit/json_spirit_reader.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/json_spirit/json_spirit_value.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/json_spirit/json_spirit_writer.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/json_spirit/json_spirit_tools.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/basic_sys_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/Binary_Util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/exit.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/heap.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/inline_file_provider.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/integer_mapping.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/LexicographicalIterator.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/mpi_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/SimulateMPI.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/PyExitCallback.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/recent_history_queue.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/static_database.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/string_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/curl.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/options/mpi_stderr.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/options/OptionCollection.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/options/ResidueChainVectorOption.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/sql_database/DatabaseSessionManager.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/sql_database/types.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/boinc/boinc_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/icstream.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/izstream.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/ocstream.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/ozstream.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/FileContentsMap.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/file/file_sys_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/file/FileName.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/file/gzip_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/file/PathName.os -Lexternal/lib -Lbuild/src/release/linux/3.13/64/x86/gcc/4.8/mpi -Lsrc -Lbuild/external/release/linux/3.13/64/x86/gcc/4.8/mpi -Lexternal -L/usr/lib -L/usr/local/lib -lObjexxFCL -lz -lcppdb -lsqlite3
/usr/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/libutility.so] Error 1
scons: building terminated because of errors.

Also,I retried to install after copy command at /main/source/tools/build
cp site.settings.topsail site.settings
cd brabra/main/source/
./scons.py -j4 mode=release bin extras=mpi

Immediately,I got follow errors

root@tan-VirtualBox:/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source# ./scons.py -j4 mode=release bin extras=mpi
scons: Reading SConscript files …
Traceback (most recent call last):
File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/SConstruct”, line 150, in main
build = SConscript(“tools/build/setup.py”)
File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py”, line 614, in __call__
return method(*args, **kw)
File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/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 “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/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 “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/tools/build/setup.py”, line 421, in
build = setup()
File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/tools/build/setup.py”, line 413, in setup
build.settings = setup_build_settings(build.options)
File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/tools/build/setup.py”, line 210, in setup_build_settings
site = Settings.load(“site.settings”, “settings”)
File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/tools/build/settings.py”, line 86, in load
execfile(file, settings)
File “site.settings”, line 27, in
File “/usr/lib/python2.7/UserDict.py”, line 23, 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.

What should I do to solve this problem?

Best regards

[Anonymous]

Several things going on here.

The first is you need to have the zlib libraries installed. On Ubuntu this should be the zlib1g-dev package.

The second issue you’re running into is that you don’t have the environment variables set up appropriately for your MPI compile. There’s a number of environment variables you need to specify.

First off, you need to have the path to the MPI compiler in your PATH environment variable. This probably will happen by default, if you install it to the standard location.

Next, you need to have the path to the MPI libraries in your INCLUDE environment variable. This is what you’re missing with the second error. You’ll need to install the libopenmpi-dev package on Ubuntu to get these headers. That won’t fix the environment variable issue, though. You’ll have to set it to something like “/usr/lib/openmpi/include/” yourself.

The final environment variable to worry about is LD_LIBRARY_PATH. This may or may not be set appropriately yet. You want to make sure that the path /usr/lib/ (Where the MPI shared libraries should be) is in it.

[Author]

Posts