Hi Elie Glad to know you solved the problem. Congrats!
Hopefully our discussion will help other EPW+QE users that subscribe to the Open MPI list troubleshoot EPW problems. Indeed, the Quantum Espresso (QE) configure script seems to miss the correct library names of the Intel MKL libraries (which unfortunately are non-standard), a problem that your fix below addressed correctly. Likewise for the fftw, which in my computer it seems to have built from scratch in a QE subdirectory which has the fftw source code, or at least the required part of it. As for you TOPDIR directory setting, I didn't set that up. My impression is that putting the EPW main directory right below the QE top directory, would take care of this, at least that seems to have been what happened in my setup, but I may have missed some detail of how things are laid out in your computer. Anyway, not knowing how things are organized and the libraries location in your computer it was hard for me to guess these things right. Good luck to you and to your solid state Physics research in Rondonia. Gus Correa On Sep 6, 2014, at 11:32 AM, Elio Physics wrote: > Hello Gus, > > Thanks once again for your help and guidance. I just want to let you know > that I was able to resolve the problem; I actually changed the locations of > the libraries before configuring; for example I set: > > BLAS_LIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core > LAPACK_LIBS = > /opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_lapack95_lp64.a > FFT_LIBS=-L/opt/scilibs/FFTW/fftw-3.2.1_Bull.9005/lib -lfftw3 > > and also to link espresso libs with the plugins, i added the following line: > > TOPDIR=/home_cluster/fis718/...../espresso-4.0.3/ > > The compilation went with no errors and epw.x was produced.. Once again, > thanks for your support and help. > > Regards > > ELIO MOUJAES > > > > > > Date: Thu, 4 Sep 2014 12:48:44 -0400 > > From: g...@ldeo.columbia.edu > > To: us...@open-mpi.org > > Subject: Re: [OMPI users] compilation problem with ifort > > > > Hi Elie > > > > The executable generated in my computer will be useless to you, > > because these days most if not all libraries linked to an executable are > > dynamic/shared libraries. > > You won't have the same in your computer, or the equivalent will be > > located in different places, may be from different versions, etc. > > (E.g. your Intel compiler libraries will be from a different version, > > in a different location, and likewise for OpenMPI libraries etc.) > > Take any executable that you may have in your computer and do "ldd > > exectuable_name" to see the list of shared libraries. > > > > The error you reported suggests a misconfiguration of Makefiles, > > or better, a mispositioning of directories. > > > > ** > > > > First thing I would try is to start fresh. > > Delete or move the old directory trees, > > download everything again on blank directories, > > and do the recipe all over again. > > Leftovers of previous compilations are often a hurdle, > > so you do yourself a favor by starting over from scratch. > > > > ** > > Second *really important* item to check: > > > > The top directories of QE and EPW *must* follow this hierarchy: > > > > espresso-4.0.3 > > |-- EPW-3.0.0 > > > > Is this what you have? > > The EPW web site just hints this in their recipe step 3. > > The Makefiles will NOT work if this directory hierarchy is incorrect. > > > > The error you reported in your first email *suggests* that the Makefiles > > in the EPW tarball are not finding the Makefiles in the QE tarball, > > which indicates that the the directories may not have a correct relative > > location. > > > > I.e. the EPW top directory must be right under the QE top directory. > > > > ** > > > > Third thing, is that you have to follow the recipe strictly (and on > > the EPW web site there seems to be typos and omissions): > > > > 1) untar the QE tarball: > > > > tar -zxf espresso-4.0.3.tar.gz > > > > 2) move the EPW tarball to the QE top directory produced by step 1 > > above, something like this: > > > > mv EPW-3.0.0.tar.gz espresso-4.0.3 > > > > 3) untar the EPW tarball you copied/moved in step 2 above, > > something like this: > > > > cd espresso-4.0.3 > > tar -zxf EPW-3.0.0.tar.gz > > > > 4) Set up your OpenMPI environment (assuming you are using OpenMPI > > and that it is not installed in a standard location such as /usr/local): > > > > > > [bash/sh] > > export PATH=/your/openmpi/bin:$PATH > > export LD_LIBRARY_PATH=/your/openmpi/lib:$LD_LIBRARY_PATH > > > > [tcsh/csh] > > setenv PATH /your/openmpi/bin:$PATH > > setenv LD_LIBRARY_PATH /your/openmpi/lib:$LD_LIBRARY_PATH > > > > 5) configure espresso-4.0.3, i.e, assuming you already are in the > > espresso-4.0.3, do: > > > > ./configure CC=icc F77=ifort > > > > (assuming you are using Intel compilers, and that you compiled OpenMPI > > with them, if you did > > not, say, if you used gcc and gfortran, use CC=gcc FC=gfortran instead) > > > > 6) Run "make" on the top EPW directory: > > > > cd EPW-3.0.0 > > make > > > > When you configure QE it doesn't compile anything. > > It just generates/sets up a bunch of Makefiles in the QE directory tree. > > > > When you do "make" on the EPW-3.0.0 directory the top Makefile just > > says (cd src; make). > > If you look into the "src" subdirectory you will see that the Makefile > > therein points to library and include directories two levels above, > > which means that they are in the *QE* directory tree: > > > > ********* > > IFLAGS = -I../../include > > MODFLAGS = -I./ -I../../Modules -I../../iotk/src \ > > -I../../PW -I../../PH -I../../PP > > LIBOBJS = ../../flib/ptools.a ../../flib/flib.a \ > > ../../clib/clib.a ../../iotk/src/libiotk.a > > W90LIB = ../../W90/libwannier.a > > ********** > > > > Hence, if your QE directory is not immediately above your EPW directory > > everything will fail, because the EPW Makefile won't be able to find > > the bits and parts of QE that it needs. > > And this is *exactly what the error message in your first email showed*, > > a bunch of object files that were not found. > > > > *** > > > > Sorry, but I cannot do any better than this. > > I hope this helps, > > Gus Correa > > > > On 09/03/2014 08:59 PM, Elio Physics wrote: > > > Ray and Gus, > > > > > > Thanks a lot for your help. I followed Gus' steps. I still have the same > > > problem for the compilation (I didnt check the libraries part though!). > > > The executables for quantum espresso work pretty fine. I have got them > > > in espresso-4.0.3/bin: > > > dynmat.x iotk iotk_print_kinds.x iotk.x matdyn.x ph.x pw.x q2r.x. > > > The problem are the EPW executables and I dont understand why. > > > > > > Gus do me a favor: can u send me all the EPW executables that you have > > > produced, in the epw.x? I guess this resolves the problem for the moment. > > > > > > Regards > > > > > > ELIO > > > > > > > Date: Wed, 3 Sep 2014 19:45:32 -0400 > > > > From: g...@ldeo.columbia.edu > > > > To: us...@open-mpi.org > > > > Subject: Re: [OMPI users] compilation problem with ifort > > > > > > > > Hi Elio > > > > > > > > For what it is worth, I followed the instructions on > > > > the EPW web site, and the program compiled flawlessly. > > > > Sorry, I don't know how to use/run it, > > > > don't have the time to learn it, and won't even try. > > > > > > > > ** > > > > > > > > 1) Environment: > > > > > > > > If your MPI/OpenMPI is not installed in a standard location, > > > > you need to setup these environment variables: > > > > > > > > [bash/sh] > > > > export PATH=/your/openmpi/bin:$PATH > > > > export LD_LIBRARY_PATH=/your/openmpi/lib:$LD_LIBRARY_PATH > > > > > > > > [tcsh/csh] > > > > setenv PATH /your/openmpi/bin:$PATH > > > > setenv LD_LIBRARY_PATH /your/openmpi/lib:$LD_LIBRARY_PATH > > > > > > > > ** > > > > > > > > 2) Configuring QE: > > > > > > > > In step 2, I separated the final configure step, to set the compilers to > > > > Intel. > > > > I used OpenMPI compiled with intel, hence I > > > > configured QuantumEspresso with Intel compilers: > > > > > > > > ./configure CC=icc FC=ifort > > > > > > > > NOTE: You may need to use tar zxf ... instead of tar xfz ... > > > > > > > > ** > > > > > > > > 3) Untar EPW in the correct location > > > > > > > > Step 3 should be as below. > > > > (You need to untar EPW inside the espresso-4.0.3 directory. > > > > Could this have been the problem for you?): > > > > > > > > > > > > cp EPW-3.0.0.tar.gz espresso-4.0.3/ > > > > cd espresso-4.0.3/ > > > > tar zxf EPW-3.0.0.tar.gz > > > > > > > > ** > > > > > > > > 4) Run make to compile EPW > > > > > > > > The compilation in step 4 takes a while, is long, but works fine, > > > > and produces the epw.x executable as expected. > > > > > > > > ** > > > > > > > > 5) Old version issue, perhaps? > > > > > > > > Also, you said you "installed the older version of quantum espresso". > > > > Could this have been the problem (older version)? > > > > Did you try the latest QE (4.0.3), and the latest EPW (3.0.0), > > > > as per the recipe on the EPW web site? > > > > > > > > http://epw.org.uk/Main/DownloadAndInstall > > > > > > > > ** > > > > > > > > I hope this helps, > > > > Gus Correa > > > > > > > > > > > > > > > > > > > > On 09/03/2014 06:48 PM, Elio Physics wrote: > > > > > I have already done all of the steps you mentioned. I have > > > installed the > > > > > older version of quantum espresso, configured it and followed all the > > > > > steps on the EPW website when I got that error in the last steo; In > > > fact > > > > > I do have the latest version of quantum espresso but since I work with > > > > > electron phonon and EPW seemed really promising and less time > > > consuming, > > > > > I decided to give it a try. > > > > > > > > > > The reason I have asked my question in this forum because once I had a > > > > > similar "compiler" issue (not the same as this one) and when i asked > > > > > on > > > > > the Quantum Espresso (QE) website, one of the answers was, this is not > > > > > the right since this is a compiler problem not a QE issue so I was > > > > > really trying to avoid such answers. > > > > > > > > > > Anyhow, I guess you are absolutely right. I will try to e-mail the EPW > > > > > people and explain the situation; after all they should be able to > > > help. > > > > > Thanks for your advice and time. > > > > > > > > > > ELIO MOUJAESS > > > > > University of Rondonia > > > > > Brasil > > > > > > > > > > > Date: Wed, 3 Sep 2014 18:19:25 -0400 > > > > > > From: g...@ldeo.columbia.edu > > > > > > To: us...@open-mpi.org > > > > > > Subject: Re: [OMPI users] compilation problem with ifort > > > > > > > > > > > > It is hard to tell why, but the object files (yes a2f.o, etc) > > > > > > seem not to have been compiled from the corresponding source files > > > > > > (a2f.f90 or similar). > > > > > > > > > > > > In general the executable (your epw.x) is compiled only after all > > > > > > the pre-requisite object files (the .o) and modules (the .mod) > > > > > > have been compiled already. > > > > > > In many cases there is not only one Makefile, but a chain/tree of > > > > > > them, to compile the code in the source directory tree (under src). > > > > > > > > > > > > Also, it is a bit awkward that you don't seem to > > > > > > have configured anything, > > > > > > i.e., telling where MPI was installed, etc, > > > > > > but that may just not be in your email. > > > > > > > > > > > > Phonons is not my league, just trying to help, but afraid I may > > > > > > not take you in the right direction. > > > > > > > > > > > > Did you do the installation as per the EPW web site? (I just > > > found it): > > > > > > http://epw.org.uk/Main/DownloadAndInstall > > > > > > It seems to require QuantumExpresso. > > > > > > Did you get it, configure it, etc? > > > > > > > > > > > > Do they have a mailing list or bulletin board where you could get > > > > > > specific help for their software? > > > > > > (Either on EPW or on QuantumExpresso (which seems to be required): > > > > > > http://www.quantum-espresso.org/) > > > > > > That would probably be the right forum to ask your questions. > > > > > > > > > > > > My two cents, > > > > > > Gus Correa > > > > > > > > > > > > > > > > > > On 09/03/2014 05:51 PM, Elio Physics wrote: > > > > > > > This was the first error yes. What do you mean other files are > > > missing? > > > > > > > Do you mean the atom.o, basic_algebra_routines.o.......? Well > > > the f90 > > > > > > > files present in the src subdirectory start from a2f.90 > > > > > > > , allocate_epwq.o,...and so on... I am not also sure why there > > > is that > > > > > > > slash "\" just before the "a2f.o".... Is there a way to know > > > what is > > > > > > > going on? I mean what are the first steps? > > > > > > > > > > > > > > Thank you > > > > > > > > > > > > > > ELIO MOUJAES > > > > > > > Univeristy of Rondonia > > > > > > > Brazil > > > > > > > > > > > > > > > Date: Wed, 3 Sep 2014 17:43:44 -0400 > > > > > > > > From: g...@ldeo.columbia.edu > > > > > > > > To: us...@open-mpi.org > > > > > > > > Subject: Re: [OMPI users] compilation problem with ifort > > > > > > > > > > > > > > > > Was the error that you listed the *first* error? > > > > > > > > > > > > > > > > Apparently various object files are missing from the > > > > > > > > ../../Modules/ directory, and were not compiled, > > > > > > > > suggesting something is amiss even before the > > > > > > > > compilation of the executable (epw.x). > > > > > > > > > > > > > > > > On 09/03/2014 05:20 PM, Elio Physics wrote: > > > > > > > > > Dear all, > > > > > > > > > > > > > > > > > > I am really a beginner in Fortran and Linux. I was trying to > > > > > compile a > > > > > > > > > software (EPW). Everything was going fine (or maybe this is > > > what I > > > > > > > think): > > > > > > > > > > > > > > > > > > mpif90 -o epw.x ../../Modules/atom.o > > > > > > > > > ../../Modules/basic_algebra_routines.o > > > ../../Modules/cell_base.o > > > > > > > > > ../../Modules/check_stop.o ../../Modules/clocks.o > > > > > > > > > ../../Modules/constraints_module.o > > > ../../Modules/control_flags.o > > > > > > > > > ../../Modules/descriptors.o ../../Modules/dspev_drv.o > > > > > > > > > ../../Modules/electrons_base.o ../../Modules/error_handler.o > > > > > > > > > ../../Modules/exc_t.o ../../Modules/fft_base.o > > > > > > > > > ../../Modules/fft_parallel.o ../../Modules/fft_scalar.o > > > > > > > > > ../../Modules/fft_types.o ../../Modules/functionals.o > > > > > > > > > ../../Modules/input_parameters.o ../../Modules/io_files.o > > > > > > > > > ../../Modules/io_global.o ../../Modules/ions_base.o > > > > > > > ../../Modules/kind.o > > > > > > > > > ../../Modules/metagga.o > > > > > > > > > ..................................................\ a2f.o > > > > > > > > > allocate_epwq.o bcast_epw_input.o broyden.o close_epw.o > > > > > constants_epw.o > > > > > > > > > create_mesh.o create_mesh_mp.o createkmap.o dasmio.o > > > > > deallocate_epw.o > > > > > > > > > deallocate_eliashberg.o distribution.o dmebloch2wan.o > > > > > dmewan2bloch.o > > > > > > > > > dvanqq2.o dvqpsi_us3.o dvqpsi_us_only3.o dynbloch2wan.o > > > > > dynwan2bloch.o > > > > > > > > > eliashberg.o > > > > > > > > > > > > > > > > > > Then I get the following error: > > > > > > > > > ifort: error #10236: File not found: 'a2f.o' > > > > > > > > > ifort: error #10236: File not found: 'allocate_epwq.o' > > > > > > > > > ifort: error #10236: File not found: 'bcast_epw_input.o' > > > > > > > > > ifort: error #10236: File not found: 'broyden.o' > > > > > > > > > ifort: error #10236: File not found: 'close_epw.o' > > > > > > > > > ifort: error #10236: File not found: 'constants_epw.o' > > > > > > > > > ifort: error #10236: File not found: 'create_mesh.o' > > > > > > > > > ifort: error #10236: File not found: 'create_mesh_mp.o' > > > > > > > > > ifort: error #10236: File not found: 'createkmap.o' > > > > > > > > > ifort: error #10236: File not found: 'dasmio.o' > > > > > > > > > ifort: error #10236: File not found: 'deallocate_epw.o' > > > > > > > > > ifort: error #10236: File not found: 'deallocate_eliashberg.o' > > > > > > > > > ifort: error #10236: File not found: 'distribution.o' > > > > > > > > > ifort: error #10236: File not found: 'dmebloch2wan.o' > > > > > > > > > ifort: error #10236: File not found: 'dmewan2bloch.o' > > > > > > > > > ifort: error #10236: File not found: 'dvanqq2.o' > > > > > > > > > ifort: error #10236: File not found: 'dvqpsi_us3.o' > > > > > > > > > ifort: error #10236: File not found: 'dvqpsi_us_only3.o' > > > > > > > > > ifort: error #10236: File not found: 'dynbloch2wan.o' > > > > > > > > > ifort: error #10236: File not found: 'dynwan2bloch.o' > > > > > > > > > ifort: error #10236: File not found: 'eliashberg.o' > > > > > > > > > ifort: error #10236: File not found: 'eliashbergcom. > > > > > > > > > make[1]: *** [epw] Error 1 > > > > > > > > > make[1]: Leaving directory > > > > > > > > > `/home_cluster/fis718/eliemouj/espresso-4.0.3/EPW-3.0.0/src' > > > > > > > > > make: *** [epw] Error 2 > > > > > > > > > > > > > > > > > > I reckon that there is an error in the Makefile. However the > > > > > Makefile > > > > > > > > > content is just: > > > > > > > > > "default: epw > > > > > > > > > > > > > > > > > > all: epw > > > > > > > > > > > > > > > > > > epw: > > > > > > > > > (cd src ; make ) > > > > > > > > > (cd bin ; ln -fs ../src/epw.x . ) > > > > > > > > > > > > > > > > > > clean: > > > > > > > > > cd src ; rm -f *.o *.mod *.F90 *~ > > > > > > > > > > > > > > > > > > release: > > > > > > > > > cd ../ ; cp -r EPW EPW-release; cd EPW-release ; \ > > > > > > > > > rm -f src/*.o src/*.mod src/*.F90 src/*~ ; \ > > > > > > > > > rm bin/*.x ; \ > > > > > > > > > rm -rf examples/*/epw/out/* examples/*/epw/tmp/* \ > > > > > > > > > examples/*/phonons/out/* examples/*/phonons/tmp/* \ > > > > > > > > > examples/*/phonons/save/* ; \ > > > > > > > > > rm -rf .svn */.svn */*/*.svn */*/*/*.svn */*/*/*/*.svn > > > > > > > > > cd .. ; tar cfz EPW/EPW-release.tgz EPW-release ; \ > > > > > > > > > rm -rf EPW-release ; cd EPW " > > > > > > > > > > > > > > > > > > Please can anyone help me and guide me how to fix this error > > > > > step by > > > > > > > > > step as I am no FOrtran or Linux professional > > > > > > > > > > > > > > > > > > Regards > > > > > > > > > > > > > > > > > > ELIO MOUJAES > > > > > > > > > University of Rondonia > > > > > > > > > Brazil > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > users mailing list > > > > > > > > > us...@open-mpi.org > > > > > > > > > Subscription: > > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > > > > Link to this post: > > > > > > > http://www.open-mpi.org/community/lists/users/2014/09/25253.php > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > users mailing list > > > > > > > > us...@open-mpi.org > > > > > > > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > > > Link to this post: > > > > > > > http://www.open-mpi.org/community/lists/users/2014/09/25254.php > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > users mailing list > > > > > > > us...@open-mpi.org > > > > > > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > > Link to this post: > > > > > http://www.open-mpi.org/community/lists/users/2014/09/25255.php > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > users mailing list > > > > > > us...@open-mpi.org > > > > > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > Link to this post: > > > > > http://www.open-mpi.org/community/lists/users/2014/09/25256.php > > > > > > > > > > > > > > > _______________________________________________ > > > > > users mailing list > > > > > us...@open-mpi.org > > > > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > Link to this post: > > > http://www.open-mpi.org/community/lists/users/2014/09/25257.php > > > > > > > > > > > > > _______________________________________________ > > > > users mailing list > > > > us...@open-mpi.org > > > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > Link to this post: > > > http://www.open-mpi.org/community/lists/users/2014/09/25260.php > > > > > > > > > _______________________________________________ > > > users mailing list > > > us...@open-mpi.org > > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > > Link to this post: > > > http://www.open-mpi.org/community/lists/users/2014/09/25262.php > > > > > > > _______________________________________________ > > users mailing list > > us...@open-mpi.org > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > Link to this post: > > http://www.open-mpi.org/community/lists/users/2014/09/25271.php > _______________________________________________ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2014/09/25289.php
