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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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apbs cmake compilation issue #527

Closed ktamiola closed 4 years ago

ktamiola commented 4 years ago

Ladies an gents, I wanted to report an apbs compilation issue.

Steps to reproduce:

  1. Clone the repo.
  2. Do git module init and updates.
  3. Start cmake src/

Cmake version: cmake version 3.15.2

-- Adding apbs_generic
-- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c
-- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h
-- With internal header files 
-- With library dependencies 
-- Added apbs_generic
-- Adding apbs_pmgc
-- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c
-- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h
-- With internal header files 
-- With library dependencies 
-- Added apbs_pmgc
-- Adding apbs_mg
-- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c
-- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h
-- With internal header files 
-- With library dependencies apbs_generic;apbs_pmgc
-- Added apbs_mg
-- Adding apbs_routines
-- With source files routines.c
-- With external header files 
-- With internal header files 
-- With library dependencies 
-- Added apbs_routines
-- 
--  
-- APBS Libraries: 
-- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines
--  
CMake Error: File /src/.config/apbscfg.h.in does not exist.
CMake Error at CMakeLists.txt:70 (configure_file):
  configure_file Problem configuring file

CMake Error at CMakeLists.txt:81 (INSTALL):
  INSTALL FILES given no DESTINATION!

-- 
-- Configuring incomplete, errors occurred!
See also "/mnt/c55adb58-05c8-4471-b80b-cb53ae5734e8/research/apbs-pdb2pqr/apbs/CMakeFiles/CMakeOutput.log".
kozlac commented 4 years ago

Hello @ktamiola, just based on what you posted it seems to me that you are trying to build in a directory with no writing permissions. Could you verify this? And if it is not the case, could you provide more details (i.e. os, version, installation location, etc...)? Thanks!

kozlac commented 4 years ago

Hello @ktamiola, looking closer at the output you posted the problem is that you are calling the cmake on the apbs/src/ folder. This cause cmake to see the CMakeLists.txt in apbs/src/ but not the top-level one in the /apbs folder. I would recommend you doing an out of source build. That is, create a folder somewhere else and call cmake on the top-level apbs folder. For example, if my current directory has the following structure: current_dir$ ls build apbs pdb2pqr

Then from inside build: current_dir$ cd build currrent_dir/build$ cmake ../apbs/

Then run make after cmake completes successfully.

Please let me know if this resolves your issue. Thanks!!

ktamiola commented 4 years ago

Thank you so much @kozlac . Indeed, a mistake was made at my end. I have sorted it out.

ktamiola commented 4 years ago

Thank You so much for your help Juan. Indeed, the mistake was made on my end.

On Tue, Aug 27, 2019 at 7:28 PM Juan notifications@github.com wrote:

Hello @ktamiola https://github.com/ktamiola, looking closer at the output you posted the problem is that you are calling the cmake on the apbs/src/ folder. This cause cmake to see the CMakeLists.txt in apbs/src/ but not the top-level one in the /apbs folder. I would recommend you doing an out of source build. That is, create a folder somewhere else and call cmake on the top-level apbs folder. For example, if my current directory has the following structure: current_dir$ ls build apbs pdb2pqr

Then from inside build: current_dir$ cd build currrent_dir/build$ cmake ../apbs/

Then run make after cmake completes successfully.

Please let me know if this resolves your issue. Thanks!!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Electrostatics/apbs-pdb2pqr/issues/527?email_source=notifications&email_token=ABWFRIN3XEQL24EBQVGXNODQGVP5RA5CNFSM4IPKFG42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5IQITY#issuecomment-525403215, or mute the thread https://github.com/notifications/unsubscribe-auth/ABWFRIJBKJA4OEICA6XVDEDQGVP5RANCNFSM4IPKFG4Q .

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