Re: [ESPResSo-users] Error in python code checks

[Michael Klatt]

Dear Rudolf, Dear Henri,

Thank you very much for your e-mails!
I appreciate your quick help very much.

Unfortunately, there seems to be still some conflict.

It is indeed my laptop (Xubuntu 16.04) where I have been trying to 
compile espresso. So, I can install software freely. My laptop has two 
cores and each core can have two threads. Could the problem be caused if 
pypresso tries to call more than four threads?

If not, here is an update on the error reports:

I used new (that is empty) build directories and libboost-mpi-dev was 
already installed.

The packages "python-h5py python-enum libhdf5-openmpi-dev" were actually 
missing. So I installed them and built espresso in a completely new 
directory.

There is still an error message (although it seems to have slightly 
changed), see the postscript.

I have attached the output of cmake. Is that what you actually meant?
Do you need anything else?

Concerning the Docker files. I am sorry, but I am not used to Docker 
files. How should I used them?

Thank you very much once more for your help!

Best regards,

Michael

$ make check
[  0%] Built target myconfig
[  0%] Built target check_myconfig
[  0%] Built target EspressoConfig
Scanning dependencies of target link_cell_test
[  0%] Building CXX object 
src/core/unit_tests/CMakeFiles/link_cell_test.dir/link_cell_test.cpp.o
[  0%] Linking CXX executable link_cell_test
[  0%] Built target link_cell_test
Scanning dependencies of target Cache_test
[  1%] Building CXX object 
src/core/unit_tests/CMakeFiles/Cache_test.dir/Cache_test.cpp.o
[  1%] Linking CXX executable Cache_test
[  1%] Built target Cache_test
Scanning dependencies of target None_test
[  1%] Building CXX object 
src/core/unit_tests/CMakeFiles/None_test.dir/None_test.cpp.o
[  2%] Linking CXX executable None_test
[  2%] Built target None_test
Scanning dependencies of target all_compare_test
[  3%] Building CXX object 
src/core/unit_tests/CMakeFiles/all_compare_test.dir/all_compare_test.cpp.o
[  3%] Linking CXX executable all_compare_test
CMakeFiles/all_compare_test.dir/all_compare_test.cpp.o: In function 
`bool Utils::Mpi::all_compare<int>(boost::mpi::communicator const&, int 
const&)':
all_compare_test.cpp:(.text._ZN5Utils3Mpi11all_compareIiEEbRKN5boost3mpi12communicatorERKT_[_ZN5Utils3Mpi11all_compareIiEEbRKN5boost3mpi12communicatorERKT_]+0x3e): 
undefined reference to `boost::mpi::communicator::operator int() const'
all_compare_test.cpp:(.text._ZN5Utils3Mpi11all_compareIiEEbRKN5boost3mpi12communicatorERKT_[_ZN5Utils3Mpi11all_compareIiEEbRKN5boost3mpi12communicatorERKT_]+0xa2): 
undefined reference to `boost::mpi::communicator::operator int() const'
collect2: error: ld returned 1 exit status
src/core/unit_tests/CMakeFiles/all_compare_test.dir/build.make:126: 
recipe for target 'src/core/unit_tests/all_compare_test' failed
make[3]: *** [src/core/unit_tests/all_compare_test] Error 1
CMakeFiles/Makefile2:1599: recipe for target 
'src/core/unit_tests/CMakeFiles/all_compare_test.dir/all' failed
make[2]: *** [src/core/unit_tests/CMakeFiles/all_compare_test.dir/all] 
Error 2
CMakeFiles/Makefile2:107: recipe for target 'CMakeFiles/check.dir/rule' 
failed
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
Makefile:186: recipe for target 'check' failed
make: *** [check] Error 2

-------------------------------------------------------------------------

P.P.S. $ ./pypresso
Python 2.7.14 |Anaconda, Inc.| (default, Dec  7 2017, 17:05:42)
[GCC 7.2.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import espressomd
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File 
"/home/mklatt/postdoc-working/workbench/espresso/build/src/python/espressomd/__init__.py", 
line 23, in <module>
    import espressomd._init
ImportError: 
/home/mklatt/postdoc-working/workbench/espresso/build/src/core/io/writer/h5md/libH5mdCore.so: 
undefined symbol: 
_ZN5boost3mpi6detail19packed_archive_recvEiiiRNS0_15packed_iarchiveER10MPI_Status
>>>




On 29.03.2018 01:57, Henri Menke wrote:
> On Wed, 2018-03-28 at 20:55 +0200, Michael Klatt wrote:
> > Dear all,
> >
> > I am new user of ESPResSo. Unfortunately, I can only run the TCL
> > scripts, but pypresso causes errors that I cannot resolve on my own.
> >
> > Is there a TCL counterpart of the python minimize_energy functionality?
> > If not may I ask for your help to resolve my problems with pypresso?
> > Thank you very much!
> >
> > In the following, I summarize the error reports (full error reports are
> > included in the postscript).
> >
> > I am using Xubuntu 16.04. Neither the latest release (3.3.1) of ESPResSo
> > nor cloning the python branch on GitHub worked. Resolving the problems
> > for any of the two would suffice.
>
> I just compiled ESPResSo on a naked Ubuntu 16.04 to see if I can reproduce your
> issue, but I couldn't.  Here are my steps:
>
> apt-get update
> apt-get install build-essential cmake git openmpi-bin libfftw3-dev libboost-dev 
> libboost-serialization-dev libboost-mpi-dev libboost-filesystem-dev 
> libboost-test-dev cython python python-numpy python-h5py python-enum 
> libhdf5-openmpi-dev libhdf5-openmpi-10 libhdf5-10
> git clone https://github.com/espressomd/espresso.git
> cd espresso/
> mkdir build
> cd build/
> cmake ..
> make -j 16
>
> Then I can run ./pypresso
>
> > > > import espressomd
> > > > print(espressomd.features())
> ['BOND_ANGLE', 'BUCKINGHAM', 'COLLISION_DETECTION', 'CONSTRAINTS', 
> 'ELECTROSTATICS', 'EXCLUSIONS', 'EXTERNAL_FORCES', 'FFTW', 'GAUSSIAN', 
> 'GHOSTS_HAVE_BONDS', 'H5MD', 'HERTZIAN', 'LANGEVIN_PER_PARTICLE', 'LATTICE', 
> 'LB', 'LB_BOUNDARIES', 'LENNARD_JONES', 'LENNARD_JONES_GENERIC', 'LJCOS', 
> 'LJCOS2', 'MASS', 'MORSE', 'NPT', 'P3M', 'PARTIAL_PERIODIC', 'SOFT_SPHERE', 
> 'TABULATED']
>
>
>
> > -------------------------------------------------------------------------
> >
> > (1) When I compiled the latest release (3.3.1), "import espressomd"
> > causes no problems, but "print(espressomd.features())" throws an error:
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > AttributeError: 'module' object has no attribute 'features'
> >
> > -------------------------------------------------------------------------
> >
> > (2) Last week, I have cloned the python branch of ESPResSo and followed
> > the instructions for installation from the ESPResSo documentation.
> >
> > "make install" was completed without errors.
> > However, "make check" reported a problem:
> > undefined reference to `boost::mpi::communicator::operator int() const'
> >
> > When I import espressomd in "pypresso", the following error is reported:
> > libcluster_analysis.so.4: undefined symbol:
> > _ZNK5boost3mpi12communicatorcviEv
> >
> > -------------------------------------------------------------------------
> >
> > Thank you very much once more for your help!
> >
> > Best regards,
> >
> > Michael
> >
> > -------------------------------------------------------------------------
> >
> > P.S. Error when invoking code checks:
> >
> > $ make check
> > [ 2%] Built target myconfig
> > [ 2%] Built target check_myconfig
> > [ 2%] Built target EspressoConfig
> > [ 2%] Built target link_cell_test
> > [ 2%] Built target Cache_test
> > [ 2%] Built target None_test
> > [ 2%] Linking CXX executable all_compare_test
> > CMakeFiles/all_compare_test.dir/all_compare_test.cpp.o: In function
> > `bool Utils::Mpi::all_compare<int>(boost::mpi::communicator const&, int
> > const&)':
> > all_compare_test.cpp:(.text._ZN5Utils3Mpi11all_compareIiEEbRKN5boost3mpi12comm
> > unicatorERKT_[_ZN5Utils3Mpi11all_compareIiEEbRKN5boost3mpi12communicatorERKT_]
> > +0x3e):
> > undefined reference to `boost::mpi::communicator::operator int() const'
> > all_compare_test.cpp:(.text._ZN5Utils3Mpi11all_compareIiEEbRKN5boost3mpi12comm
> > unicatorERKT_[_ZN5Utils3Mpi11all_compareIiEEbRKN5boost3mpi12communicatorERKT_]
> > +0xa2):
> > undefined reference to `boost::mpi::communicator::operator int() const'
> > collect2: error: ld returned 1 exit status
> > src/core/unit_tests/CMakeFiles/all_compare_test.dir/build.make:121:
> > recipe for target 'src/core/unit_tests/all_compare_test' failed
> > make[3]: *** [src/core/unit_tests/all_compare_test] Error 1
> > CMakeFiles/Makefile2:1510: recipe for target
> > 'src/core/unit_tests/CMakeFiles/all_compare_test.dir/all' failed
> > make[2]: *** [src/core/unit_tests/CMakeFiles/all_compare_test.dir/all]
> > Error 2
> > CMakeFiles/Makefile2:107: recipe for target 'CMakeFiles/check.dir/rule'
> > failed
> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > Makefile:186: recipe for target 'check' failed
> > make: *** [check] Error 2
> >
> > -------------------------------------------------------------------------
> >
> > P.P.S. Error when importing espressomd in "pypresso":
> >
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > File "/usr/local/lib/python2.7/site-packages/espressomd/__init__.py",
> > line 23, in <module>
> > import espressomd._init
> > ImportError: /home/mklatt/[...path to
> > espresso...]/espresso/build/src/core/cluster_analysis/libcluster_analysis.so.4
> > :
> > undefined symbol: _ZNK5boost3mpi12communicatorcviEv

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cmake-output.txt
Description: Text document