Unable to finish XTP qm calculations tutorial

[Thibaut Wohrer]

Hello,

I have been experiencing issues when running the tutorial for QMMM calculation the XTP module as described here https://www.votca.org/xtp-tutorials/QMMM_GROMACS.html 

Specifically upon reaching the final section of the actual QMMM calculations, when inputting the line 

xtp_parallel -e qmmm -o OPTIONFILES/qmmm.xml -p 2 -f state.hdf5 -j run

The first calculation runs normally for job ID 0 but moving to job ID 1 leads to the following error.  

ERROR: Job file incomplete.

 Job with id 1 is not finished. Check your job file for FAIL, AVAILABLE, or ASSIGNED. Exiting

terminate called after throwing an instance of 'std::runtime_error'

  what():  Error: filters is not found

This error occurs on a normal machine and for a PBS submitted script. This error also occurs regardless of using 

sed -i '0,/COMPLETE/s/COMPLETE/AVAILABLE/' qmmm_jobs.xml

and this type of error does not occur in any of the previous calculations of the tutorial.

Any help on this issue would be much appreciated!  

[Jens Wehner]

Hello,

thanks for asking. As I developed this part I probably screwed it up. I will investigate a bit and come back to it.

I think you are basically missing a default option.

How did you install votca / which version are you using?

Cheers Jens

[Thibaut Wohrer]

Hello,

I installed Votca version 1.6.2 through the installation guide using the general installation instructions.

Sincerely,

Thibaut Wohrer

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[Christoph Junghans]

On Mon, Apr 12, 2021 at 03:42 Thibaut Wohrer <tc.w...@gmail.com> wrote:

Hello,

I installed Votca version 1.6.2 through the installation  guide using the general installation instructions.

 I would try the most recent version, 2021, first!

Christoph 

 

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[Thibaut Wohrer]

Hello, 

I have attempted to reinstall Votca as its latest version but using the same steps I obtain this error

-- Checking for module 'libint2>=2.6'

--   No package 'libint2' found
CMake Error at /gpfs2/apps/spack-software/environments/default/packages/linux-rhel7-avx2_512/gcc-4.8.5/cmake-3.16.2-s6lhty27ap52usu6qkfnioit7xpbc47z/share/cmake-3.16/Modules/FindPkgConfig.cmake:463 (message):
  A required package was not found
Call Stack (most recent call first):
  /gpfs2/apps/spack-software/environments/default/packages/linux-rhel7-avx2_512/gcc-4.8.5/cmake-3.16.2-s6lhty27ap52usu6qkfnioit7xpbc47z/share/cmake-3.16/Modules/FindPkgConfig.cmake:643 (_pkg_check_modules_internal)
  xtp/CMakeLists.txt:51 (pkg_check_modules)

when using the Cmake command. As the procedure worked before I am not sure why it no longer seems to work.

Sincerely,

Thibaut Wohrer

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[Christoph Junghans]

On Tue, Apr 13, 2021 at 07:17 Thibaut Wohrer <tc.w...@gmail.com> wrote:

Hello, 

I have attempted to reinstall Votca as its latest version but using the same steps I obtain this error

-- Checking for module 'libint2>=2.6'

--   No package 'libint2' found

This above line means libint-2.6 or higher could  not be found, this is a new dependency in version 2021.

Christoph 

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[Thibaut Wohrer]

Hello and apologies for digging up this thread,

I have upgraded Votca to the newest version and have attempted to run the complete tutorial. After updating the Optionfiles I have once again encountered an issue during the last section with this time an error occurring at the line

 xtp_parallel -e qmmm -o OPTIONFILES/qmmm.xml -f state.hdf5 -j "write"

 producing

property not found: .regions

This was done using the default qmmm.xml file provided and the manual does not state any .regions options.

In addition to this I have noticed that several examples in the tutorial display error messages in the text box:

!xtp_parallel -e iqm -o OPTIONFILES/iqm.xml -f state.hdf5 -p 2 -s 0 -j run -c 1

==================================================
========   VOTCA (http://www.votca.org)   ========
==================================================

please submit bugs to https://github.com/votca/xtp/issues

xtp_parallel, version 2022-dev gitid: 59a5962 (compiled Apr 24 2021, 21:06:33)
votca_csg, version 2022-dev gitid: 59a5962 (compiled Apr 24 2021, 20:53:18)
votca_tools, version 2022-dev gitid: 59a5962 (compiled Apr 24 2021, 20:51:00)

Initializing calculator
... iqm
... ... Initialized with 1 threads.

... ... Using 2 openmp threads for 1x2=2 total threads.
1 frames in statefile, Ids are: 0
Starting at frame 0
Evaluating frame 0
Import MD Topology (i.e. frame 0) from state.hdf5
....
... iqm
MST ERR Job file = 'iqm.jobs', cache size =  1
MST ERR Initialize jobs from iqm.jobsan error occurred:
iqm.jobs: Parse error at line 2
no element found: iostream error

Is this due to a display error or is it normal?

Sincerely,

Thibaut Wohrer

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[Jens Wehner]

Hi Thibaut,

I will dig into it today. I am currently working on making all the options nice and workable, because we had some trouble in the past. 

Cheers Jens

[Jens Wehner]

Hi Thibaut,

you were right, there were several bugs in there. I made some PRs to fix these.

https://github.com/votca/xtp-tutorials/pull/73

If you want to test already checkout the tutorial_fix branch in xtp and xtp-tutorials.

So far I have only fixed the GROMACS tutorial, I have not checked LAMMPS, will do that tomorrow.

[Jens Wehner]

So apart from KMC tutorials the rest should work in master now. Sorry for the errors.

Cheers Jens

[Thibaut Wohrer]

Hello, 

When updating votca I now find the error when attempting the Cmake compilation command

  CMake Error at tools/CMakeLists.txt:109 (message):
  Could not find needed header - fstream

an error that has apparently been reported before: https://github.com/votca/csg/issues/200

I have attached the associated CmakeError.log file.  

Sincerely,

Thibaut

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[Jens Wehner]

Hi Thibaut, 

good question. Can you try a fresh install? Which system are you on? Which compiler?

[Thibaut Wohrer]

Hello Jens,

I tried a fresh install on Ubuntu using cmake/3.16.2. As this is located on a cluster I loaded the following modules before attempting a fresh install:

 module load gromacs cmake eigen/3.3.7-gcc7 fftw sqlite libxc hdf5/1.10.6-gcc7 gsl doxygen txt2tags orca

 

Thibaut

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[Jens Wehner]

Can you post the whole cmake output as well.

[Thibaut Wohrer]

The complete output is:

-- The CXX compiler identification is Intel 18.0.5.20180823
-- Check for working CXX compiler: /apps/intel/psxe_2018u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/icpc
-- Check for working CXX compiler: /apps/intel/psxe_2018u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/icpc -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS-Wall
-- Performing Test COMPILER_SUPPORTS-Wall - Success
-- Performing Test COMPILER_SUPPORTS-Wextra
-- Performing Test COMPILER_SUPPORTS-Wextra - Success
-- Performing Test COMPILER_SUPPORTS-Wpedantic
-- Performing Test COMPILER_SUPPORTS-Wpedantic - Failed
-- Performing Test COMPILER_SUPPORTS-Wshadow
-- Performing Test COMPILER_SUPPORTS-Wshadow - Success
-- Performing Test COMPILER_SUPPORTS-Wconversion
-- Performing Test COMPILER_SUPPORTS-Wconversion - Success
-- Found Git: /usr/bin/git (found version "1.8.3.1")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found Boost: /apps/boost/1.71.0/intelcc-2018.5/lib/cmake/Boost-1.71.0/BoostConfig.cmake (found suitable version "1.71.0", minimum required is "1.53.0") found components: program_options filesystem system
-- Found Python: /usr/bin/python3.6 (found suitable version "3.6.8", minimum required is "3") found components: Interpreter
-- Found Eigen3: /apps/eigen/3.3.7/gcc-7.4.0/share/eigen3/cmake
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
-- Checking for module 'fftw3'
--   Found fftw3, version 3.3.8
-- Found FFTW3: /apps/fftw3/3.3.8/intel-v18/lib/libfftw3.so
-- Looking for C++ include cassert
-- Looking for C++ include cassert - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - not found

CMake Error at tools/CMakeLists.txt:109 (message):
  Could not find needed header - fstream

-- Configuring incomplete, errors occurred!
See also "/home/users/astar/ihpc/stuthiba/scratch/ASTAR/votca-xtp-install2/builddir/CMakeFiles/CMakeOutput.log".
See also "/home/users/astar/ihpc/stuthiba/scratch/ASTAR/votca-xtp-install2/builddir/CMakeFiles/CMakeError.log".

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[Jens Wehner]

Can you  try without the intel compiler and see if it works?

Otherwise I do not have a good idea. fstream is a systems header, so that is not really votca territory.