No module named sharc.pysharc.interface

[abbottjlu]

The source code was cloned from v2.1 branch.

OS, Ubuntu 18.04

Compiled with pysharc enabled,

1. set USE_PYSHARC to false,
2. run make install in source/, 3. run make clean in source/,
3. set USE_PYSHARC to true,
4. run make install in pysharc/.

Try to run $SHARC/test.py
The test case, 17, 18

_================================================================================
|| Running test jobs... ||

/userdata/wang/app/sharc.v2.1-pysharc/bin/../tests/INPUT/LVC_pysharc
2019-11-01 16:29:37.284411 2019-11-01 16:29:37.382382 Runtime: 0:00:00.097971 Error Code: 1

/userdata/wang/app/sharc.v2.1-pysharc/bin/../tests/INPUT/LVC_pysharc_netcdf
2019-11-01 16:29:37.383196 2019-11-01 16:29:37.464266 Runtime: 0:00:00.081070 Error Code: 1

================================================================================
|| Test job analysis ||

-------------------------LVC_pysharc------------------------
Job did not finish successfully. Error code: 1

---------------------LVC_pysharc_netcdf---------------------
Job did not finish successfully. Error code: 1

================================================================================
|| Summary ||

LVC_pysharc Job did not finish
LVC_pysharc_netcdf Job did not finish_

The error log file under RUNNING_TESTS/LVC_pysharc_netcdf reports,
[wang@lab-itc LVC_pysharc_netcdf]$ ls
geom input QM run.err run.out run.sh veloc
[wang@lab-itc LVC_pysharc_netcdf]$ cat run.err
Traceback (most recent call last):
File "/userdata/wang/app/sharc.v2.1-pysharc/source/../bin/pysharc_lvc.py", line 46, in
from sharc.pysharc.interface import SHARC_INTERFACE
ImportError: No module named sharc.pysharc.interface
cp: cannot stat '/tmp/wang/TRAJ/output.*': No such file or directory
run.sh: 17: [: 1: unexpected operator
[wang@lab-itc LVC_pysharc_netcdf]$

[MFSJMenger]

You sure you set your PYTHONPATH correctly?

try after setting:

export PYTHONPATH=/userdata/wang/app/sharc.v2.1-pysharc/pysharc:$PYTHONPATH

[abbottjlu]

You sure you set your PYTHONPATH correctly?

try after setting:

export PYTHONPATH=/userdata/wang/app/sharc.v2.1-pysharc/pysharc:$PYTHONPATH

Dear MFSJmenger,
Thanks for your reply.

I tried to update the PYTHONPATH.
Now on my OS, I have got the following configuration,
[wang@lab-itc wang]$ echo $SHARC
/userdata/wang/app/sharc.v2.1-pysharc/source/../bin
[wang@lab-itc wang]$ echo $PYTHONPATH
/home/wang/app/sharc.v2.1-pysharc/pysharc:/userdata/wang/app/sharc.v2.1-pysharc/source/../lib:
[wang@lab-itc wang]$ which conda
/home/wang/anaconda2/bin/conda
[wang@lab-itc wang]$ which python
/home/wang/anaconda2/bin/python

I tried to run the test case number 17, but failed.
$SHARC/test.py reports,
-------------------------LVC_pysharc------------------------
Job did not finish successfully. Error code: 1

I found the following message from the run.err file,

Traceback (most recent call last):
  File "/userdata/wang/app/sharc.v2.1-pysharc/source/../bin/pysharc_lvc.py", line 46, in <module>
    from sharc.pysharc.interface import SHARC_INTERFACE
  File "/home/wang/app/sharc.v2.1-pysharc/pysharc/sharc/__init__.py", line 26, in <module>
    import sharc as sharc
ImportError: /userdata/wang/app/sharc.v2.1-pysharc/source/../lib/libsharc.so: undefined symbol: nc_get_vara_double
cp: cannot stat '/tmp/wang/TRAJ/output.*': No such file or directory
run.sh: 17: [: 1: unexpected operator

[MFSJMenger]

The error simply states, that it cannot find the NetCDF library against which libsharc.so was compiled.
On linux you could check that with

ldd /userdata/wang/app/sharc.v2.1-pysharc/source/../lib/libsharc.so

which would probably tell you that netcdf/hdf5 libraries are not found.
Are you sure your LD_LIBRARY_PATH (or its analogue on the Mac) is set correctly?
(On Mac I am not sure if the variables/commands are the same)

Best,
Max

[abbottjlu]

Thanks for your quick reply.
Actually I am on Linux.
My current LD_LIBRARY_PATH is,
[wang@lab-itc lib]$ echo $LD_LIBRARY_PATH
/home/wang/anaconda2/lib:/userdata/wang/app/sharc.v2.1-pysharc/source/../lib:/usr/local/cuda-10.1/lib64::/opt/chem/orca/orca411

I am sure, there is something like NetCDF and hdf5 under /home/wang/anaconda2/lib.

ldd reports the following message,
[wang@lab-itc lib]$ ldd /userdata/wang/app/sharc.v2.1-pysharc/source/../lib/libsharc.so
linux-vdso.so.1 (0x00007ffd25d9c000)
libgfortran.so.4 => /home/wang/anaconda2/lib/libgfortran.so.4 (0x00007f6d37e09000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6d376d5000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f6d374bd000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6d370cc000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f6d36e8c000)
/lib64/ld-linux-x86-64.so.2 (0x00007f6d37d12000)
[wang@lab-itc lib]$

Seems it is not linked against NetCDF?

But I am sure I compiled the source code by following these steps,

Step 1. set USE_PYSHARC to false,
Step2. run make install in source/,
Step 3. run make clean in source/,
Step 4. set USE_PYSHARC to true,
Step 5. run make install in pysharc/.

[abbottjlu]

Update.

Everything works fine on CentOS7.
blas, fftw3, lapack are provided by anaconda2.

All the other libs ( hdf5, hdf5_hl, netcdf, mfhdf, df, jpeg ) are also installed via conda install.

But, pyshac does not work on ubuntu 18.04, not sure why.