Comments (6)
bhourahine
commented on June 19, 2024
Dear Qiang,
unless you need to use the socket interface, this can be switched off in
the make.config file:
edit
# Whether the socket library (external control) should be linked.
WITH_SOCKETS := 1
to
# Whether the socket library (external control) should be linked.
WITH_SOCKETS := 0
then
make distclean
make test_dftb+
Could you tell me what
gcc --version
reports?
Regards
Ben
…On 02/01/18 23:12, Qiang Zhu wrote:
Dear developers,
I am a user of dftbplus. I randomly came across this GitHub page while I
was trying to install a new version of dftb+. Following the installation
instruction, however, I didn't manage to go through.
At the stage of compilation after copying the sys/make.x86_64-linux-gnu,
I invoked make command and met the following error message.
***@***.*** dftbplus]$ make
mkdir -p /home/qzhu/QZ/dftbplus/_build/external/fsockets
make -C /home/qzhu/QZ/dftbplus/_build/external/fsockets
-f /home/qzhu/QZ/dftbplus/external/fsockets/make.dpbuild
ROOT=/home/qzhu/QZ/dftbplus BUILDROOT=/home/qzhu/QZ/dftbplus/_build
make[1]: Entering directory
`/home/qzhu/QZ/dftbplus/_build/external/fsockets'
gcc -c -o sockets.o /home/qzhu/QZ/dftbplus/external/fsockets/sockets.c
gfortran -O2 -funroll-all-loops -fopenmp -o fsockets.o -c
/home/qzhu/QZ/dftbplus/external/fsockets/fsockets.f90
/home/qzhu/QZ/dftbplus/external/fsockets/fsockets.f90:212.43:
|call readbuffer_socket_c(sockfd, c_loc(fdata), 8_c_int * size(fdata,
kind=c 1 |
Error: Assumed-shape array 'fdata' at (1) cannot be an argument to the
procedure 'c_loc' because it is not C interoperable
/home/qzhu/QZ/dftbplus/external/fsockets/fsockets.f90:166.44:
|call writebuffer_socket_c(sockfd, c_loc(fdata), 8_c_int * size(fdata,
kind= 1 |
Error: Assumed-shape array 'fdata' at (1) cannot be an argument to the
procedure 'c_loc' because it is not C interoperable
make[1]: *** [fsockets.o] Error 1
make[1]: Leaving directory `/home/qzhu/QZ/dftbplus/_build/external/fsockets'
make: *** [external_fsockets] Error 2
Can anyone tell me how to overcome this issue with fscokets?
best regards,
Qiang
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qzhu2017
commented on June 19, 2024
Well, my gcc is as follows,
qzhu@cms:/scratch/qzhu/soft/dftbplus$ gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC)
By switching off the socket option, I pass through several stage, however it ends up with a new error which is related to the update_release.
mkdir -p /scratch/qzhu/soft/dftbplus/_build
[ -r /scratch/qzhu/soft/dftbplus/RELEASE ] && cp -a /scratch/qzhu/soft/dftbplus/RELEASE /scratch/qzhu/soft/dftbplus/_build/RELEASE
|| /scratch/qzhu/soft/dftbplus/utils/build/update_release /scratch/qzhu/soft/dftbplus/_build/RELEASE
Warning: Release could not be determined
Traceback (most recent call last):
File "/scratch/qzhu/soft/dftbplus/utils/build/update_release", line 193, in
main()
File "/scratch/qzhu/soft/dftbplus/utils/build/update_release", line 53, in main
update_release(release_file, update_release('(Unknown)'))
TypeError: update_release() missing 1 required positional argument: 'release_name'
make: *** [update_release] Error 1
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bhourahine
commented on June 19, 2024
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC)
You might have problems with some of the Fortran compilation with a
version that old. There are linux and windows pre-compiled binaries for
the 17.1 release at
http://www.dftbplus.org/download/dftb-171/
that might be an alternative.
File "/scratch/qzhu/soft/dftbplus/utils/build/update_release", line 53,
in main
update_release(release_file, update_release('(Unknown)'))
TypeError: update_release() missing 1 required positional argument:
'release_name'
make: *** [update_release] Error 1
that behaviour is a known bug, a script in the build process assumes
you have a recent version of git installed. The work-around is to create
a file called RELEASE in the top directory of the code which contains
some text:
echo "UNOFFICAL" > RELEASE
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qzhu2017
commented on June 19, 2024
Thanks for your suggestions. I will give a try on the precompiled version.
On the other hand, I also tried with intel-18.0 and more recent git version. However, it didn't work either. At the very end of linking stage. I got the following error messages.
mpif90 -O2 -ip -standard-semantics -heap-arrays 10 -I/home1/01606/qiangz/dftbplus/_build/external/xmlf90 -I/home1/01606/qiangz/dftbplus/_build/external/fsockets -I/home1/01606/qiangz/dftbplus/_build/external/dftd3 -I/home1/01606/qiangz/dftbplus/_build/external/mpifx -I/home1/01606/qiangz/dftbplus/_build/external/scalapackfx -o dftbplus.o -c dftbplus.f90
mpif90 -o dftb+ dftbplus.o main.o shift.o accuracy.o commontypes.o orbitals.o parallelks.o environment.o timerarray.o assert.o io.o globalenv.o mpifx.o timer.o mpienv.o message.o blacsenv.o scalapackfx.o mainio.o charmanip.o fifo.o fileid.o sparse2dense.o memman.o constants.o densedescr.o periodic.o sorting.o bisect.o linkedlist.o linkedlisti0.o linkedlistr1.o linkedlistr2.o linkedlisti1.o linkedlists0.o xmlf90.o linkedlistlc0.o linkedlistmc0.o linkedlistr0.o simplealgebra.o energies.o hsdutils.o tokenreader.o xmlutils.o hsdparser.o formatout.o lapackroutines.o lapack.o spin.o sccinit.o blasroutines.o blas.o mdintegrator.o velocityverlet.o thermostat.o andersentherm.o ranlux.o tempprofile.o mdcommon.o berendsentherm.o dummytherm.o nhctherm.o taggedoutput.o ipisocket.o fsockets.o logger.o optarg.o initprogram.o randomgenpool.o coulomb.o errorfunction.o diismixer.o scc.o chargeconstr.o externalcharges.o shortgamma.o nonscc.o sk.o slakocont.o slakoeqgrid.o interpolation.o dispersions.o dispiface.o dispuff.o dispcommon.o dispslaterkirkw.o dispuffdata.o dispdftd3.o dftd3.o inputdata.o pmlocalisation.o repcont.o repspline.o reppoly.o xlbomd.o extlagrangian.o linresp.o typegeometry.o simplemixer.o numderivs2.o conjgrad.o linemin.o potentials.o thirdorder.o charges.o dftbplusu.o geoopt.o steepdesc.o gdiis.o orbitalequiv.o broydenmixer.o stress.o schedule.o etemp.o hermite.o factorial.o intrinsicpr.o mixer.o andersonmixer.o elecconstraints.o angmomentum.o qm.o eigenvects.o eigensolver.o parser.o hsdutils2.o unitconversion.o oldcompat.o typegeometryhsd.o oldskdata.o densitymatrix.o populations.o repulsive.o spinorbit.o forces.o scalafxext.o -L/home1/01606/qiangz/dftbplus/_build/external/xmlf90 -lxmlf90 -L/home1/01606/qiangz/dftbplus/_build/external/fsockets -lfsockets -L/home1/01606/qiangz/dftbplus/_build/external/dftd3 -ldftd3 -L/home1/01606/qiangz/dftbplus/_build/external/mpifx -lmpifx -L/home1/01606/qiangz/dftbplus/_build/external/scalapackfx -lscalapackfx -L/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -L/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_comm_null' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to MPI_Comm_f2c'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_double' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_dblcplex'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_packed' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_op_max'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_op_maxloc' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_op_min'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_byte' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_comm_world'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_float' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_request_null'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_cplex' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_unsigned_short'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to MPI_Comm_c2f' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_double_int'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_int' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_long_long_int'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_integer' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_dblprec'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to MPI_Type_f2c' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to MPI_Op_f2c'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_op_sum' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to MPI_Op_c2f'
/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to ompi_mpi_real' /opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to MPI_Type_c2f'
make[1]: *** [dftb+] Error 1
rm parallelks.f90 dftd3.f90 hsdutils.f90 slakoeqgrid.f90 oldskdata.f90 andersentherm.f90 geoopt.f90 linkedlistr0.f90 extlagrangian.f90 spin.f90 bisect.f90 dispuff.f90 linkedlists0.f90 xlbomd.f90 mainio.f90 andersonmixer.f90 factorial.f90 intrinsicpr.f90 formatout.f90 dummytherm.f90 angmomentum.f90 broydenmixer.f90 mixer.f90 hsdparser.f90 repspline.f90 inputdata.f90 charges.f90 populations.f90 etemp.f90 mdintegrator.f90 repcont.f90 mpienv.f90 lapack.f90 sk.f90 velocityverlet.f90 simplealgebra.f90 gdiis.f90 dftbplusu.f90 densedescr.f90 chargeconstr.f90 sccinit.f90 conjgrad.f90 elecconstraints.f90 environment.f90 xmlf90.f90 steepdesc.f90 sorting.f90 berendsentherm.f90 linkedlistlc0.f90 linkedlistmc0.f90 fsockets.f90 dispersions.f90 nhctherm.f90 xmlutils.f90 fileid.f90 qm.f90 dispdftd3.f90 logger.f90 nonscc.f90 eigensolver.f90 repulsive.f90 accuracy.f90 scalapackfx.f90 timerarray.f90 hermite.f90 numderivs2.f90 unitconversion.f90 memman.f90 densitymatrix.f90 pmlocalisation.f90 lapackroutines.f90 typegeometry.f90 charmanip.f90 dispuffdata.f90 energies.f90 commontypes.f90 periodic.f90 randomgenpool.f90 tokenreader.f90 eigenvects.f90 potentials.f90 dftbplus.f90 initprogram.f90 ipisocket.f90 main.f90 optarg.f90 io.f90 linkedlistr2.f90 scalafxext.f90 linkedlisti1.f90 constants.f90 externalcharges.f90 spinorbit.f90 taggedoutput.f90 reppoly.f90 scc.f90 interpolation.f90 diismixer.f90 slakocont.f90 dispcommon.f90 orbitalequiv.f90 message.f90 fifo.f90 blacsenv.f90 stress.f90 thermostat.f90 mdcommon.f90 mpifx.f90 assert.f90 dispslaterkirkw.f90 ranlux.f90 forces.f90 simplemixer.f90 shortgamma.f90 hsdutils2.f90 oldcompat.f90 errorfunction.f90 linresp.f90 coulomb.f90 shift.f90 linkedlist.f90 orbitals.f90 tempprofile.f90 parser.f90 thirdorder.f90 linkedlistr1.f90 linemin.f90 blasroutines.f90 sparse2dense.f90 typegeometryhsd.f90 globalenv.f90 blas.f90 schedule.f90 dispiface.f90 linkedlisti0.f90 timer.f90
make[1]: Leaving directory `/home1/01606/qiangz/dftbplus/_build/prog/dftb+'
make: *** [dftb+] Error 2
I also tried intel-16 and intel17, it returned the same results.
Any suggestions?
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bhourahine
commented on June 19, 2024
On 03/01/18 02:18, Qiang Zhu wrote:
Thanks for your suggestions. I will give a try on the precompiled version.
On the other hand, I also tried with intel-18.0 and more recent git
version. However, it didn't work either. At the very end of linking
stage. I got the following error messages.
That looks like a problem with your MKL linking choices,
https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
might help.
Also, is the intention to compile the MPI parallel version of the code?
Depending on your system architecture, the shared memory openMP parallel
version might be suitable.
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bhourahine
commented on June 19, 2024
#68 Addresses the second build issue.
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