Troubles compiling siesta 4.1.b3 under intel compiler 2018

Asked by David L. Azevedo on 2018-08-02

Dear siesta users,

I have compiled siesta-4.1-b3 with intel compiler 2018, "mpiifort". The compilation finished OK. But when I ran the "ag" siesta example with mpirun -np 2, the output of siesta hangs at the line:

PhiOnMesh: nlist on node 0 = 14865
{ 0, 0}: On entry to
PDSTEDC parameter number 10 had an illegal value

What could be wrong?

If I try to run siesta just in one processor, siesta runs nice. i.e. mpirun -np 1 siesta...

Thanks for your help,

I have attached the arch.make I have used:

#
# Copyright (C) 1996-2016 The SIESTA group
# This file is distributed under the terms of the
# GNU General Public License: see COPYING in the top directory
# or http://www.gnu.org/copyleft/gpl.txt.
# See Docs/Contributors.txt for a list of contributors.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90

SIESTA_ARCH=x86_64-tumbleweed

FPP=
FPP_OUTPUT=
FC=mpiifort
RANLIB=ranlib

SYS=nag

SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
#FFLAGS= -O0 -g -check bounds -traceback
FFLAGS=-I/opt/intel/mkl/include -I/opt/intel/mkl/include/intel64/lp64 -check bounds -traceback -heap-arrays 64 -g -O2
FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DSIESTA__NO_MRRR
LDFLAGS=

ARFLAGS_EXTRA=

FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=

DUMMY_FOX= --enable-dummy
FFLAGS_DEBUG= -g -O2

BLAS_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_blas95_lp64
LAPACK_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_sequential -lmkl_core
BLACS_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_blacs_intelmpi_lp64
SCALAPACK_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_lp64

#COMP_LIBS=libsiestaLAPACK.a libsiestaBLAS.a

NETCDF_LIBS=
NETCDF_INTERFACE=

LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)

#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE= /opt/intel/impi/2018.3.222/include64

#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
atom.o: atom.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<

.c.o:
        $(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.F.o:
        $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
        $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
        $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
        $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<

When I ran ag example:

Entering directory '/home/david/downloads/siesta-4.1-b3/Obj/Tests/ag'
>>>> Running ag test...
    ==> Copying pseudopotential file for Ag...
    ==> Running SIESTA as mpirun -np 4 /home/david/downloads/siesta-4.1-b3/Obj/siesta -fdf XML.Write ../ag.fdf
Illegal argument to standard eigensolver
Stopping Program from Node: 0
make[1]: *** [../test.mk:37: completed_work] Error 1
make[1]: Leaving directory '/home/david/downloads/siesta-4.1-b3/Obj/Tests/ag'
make: *** [Makefile:113: ag] Error 2

And when I ran anneal-cont:

make tests=anneal-cont
make -C anneal-cont completed
make[1]: Entering directory '/home/david/downloads/siesta-4.1-b3/Obj/Tests/anneal-cont'
>>>> Running anneal-cont test...
    ==> Running script with SIESTA as /home/david/downloads/siesta-4.1-b3/Obj/siesta
Running script with SIESTA=mpirun -np 4 /home/david/downloads/siesta-4.1-b3/Obj/siesta
Illegal argument to standard eigensolver
Stopping Program from Node: 0
Illegal argument to standard eigensolver
Stopping Program from Node: 1
application called MPI_Abort(comm=0x84000002, 1) - process 1
Illegal argument to standard eigensolver
Stopping Program from Node: 2
application called MPI_Abort(comm=0x84000002, 1) - process 2
Illegal argument to standard eigensolver
Stopping Program from Node: 0
Illegal argument to standard eigensolver
Stopping Program from Node: 0
Illegal argument to standard eigensolver
Stopping Program from Node: 2
Illegal argument to standard eigensolver
Stopping Program from Node: 3
application called MPI_Abort(comm=0x84000002, 1) - process 3
application called MPI_Abort(comm=0x84000002, 1) - process 2
Illegal argument to standard eigensolver
Illegal argument to standard eigensolver
Stopping Program from Node: 3
Stopping Program from Node: 1
application called MPI_Abort(comm=0x84000002, 1) - process 3
application called MPI_Abort(comm=0x84000002, 1) - process 1
    ===> Script finished successfully
make[1]: Leaving directory '/home/david/downloads/siesta-4.1-b3/Obj/Tests/anneal-cont'

Question information

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Status:
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For:
Siesta Edit question
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Last query:
2018-08-02
Last reply:
2018-08-03
Nick Papior (nickpapior) said : #1

I don't have any problems using this intel version:

ifort (IFORT) 18.0.1 20171018

My arch.make is this (fit to your needs, note however that I am using openmpi and not intel-mpi):

PP = cpp -E -P -C -nostdinc
LIBS=$(ADDLIB) -lelpa -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_lapack95_lp64 -lmkl_blas95_lp64
LIBS+= -lmkl_intel_lp64 -lmkl_core -lmkl_sequential

LDFLAGS=-L/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//mkl/lib/intel64 -Wl,-rpath=/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//mkl/lib/intel64 -L/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//compiler/lib/intel64 -L/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//mkl/lib/intel64 -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/zlib/1.2.11/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/generic/numactl/2.0.11/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/libxml2/2.9.7/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/hwloc/1.11.9/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/openmpi/3.0.0/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/szip/2.1.1/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/hdf5/1.8.18/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/pnetcdf/1.8.1/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/netcdf/4.6.0/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/flook/0.7.0/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/parmetis/4.0.3/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/scotch/6.0.4/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/mumps/5.1.2/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/fftw/3.3.7/intel-18.0.1/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/elpa/2017.05.003/intel-18.0.1/lib -Wl,-rpath=/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//compiler/lib/intel64 -Wl,-rpath=/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//mkl/lib/intel64 -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/zlib/1.2.11/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/generic/numactl/2.0.11/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/libxml2/2.9.7/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/hwloc/1.11.9/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/openmpi/3.0.0/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/szip/2.1.1/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/hdf5/1.8.18/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/pnetcdf/1.8.1/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/netcdf/4.6.0/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/flook/0.7.0/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/parmetis/4.0.3/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/scotch/6.0.4/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/mumps/5.1.2/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/fftw/3.3.7/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/elpa/2017.05.003/intel-18.0.1/lib
FPPFLAGS= -I/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//compiler/include -I/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//mkl/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/zlib/1.2.11/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/generic/numactl/2.0.11/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/libxml2/2.9.7/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/hwloc/1.11.9/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/openmpi/3.0.0/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/szip/2.1.1/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/hdf5/1.8.18/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/pnetcdf/1.8.1/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/netcdf/4.6.0/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/flook/0.7.0/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/parmetis/4.0.3/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/scotch/6.0.4/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/mumps/5.1.2/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/fftw/3.3.7/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/elpa/2017.05.003/intel-18.0.1/include -DSIESTA__ELPA

.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90 .c
SIESTA_ARCH=x86_64-linux-n-62-13-32

FPP=mpif90
FPP_OUTPUT=
CC=icc
FC=mpif90
FC_SERIAL=ifort
AR=xiar
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)

FFLAGS=-m64 -fPIC -O2 -xHost -prec-div -prec-sqrt -fp-model source -qopt-prefetch
FFLAGS += #OMPPLACEHOLDER
FPPFLAGS += -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4

ARFLAGS_EXTRA=

NETCDF_INCFLAGS= -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/netcdf/4.6.0/intel-18.0.1/include
NETCDF_LIBS= -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/netcdf/4.6.0/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/netcdf/4.6.0/intel-18.0.1/lib
ADDLIB=-lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz
ADDLIB += #OMPPLACEHOLDER
INCFLAGS = -I/opt/intel/2018update1/compilers_and_libraries_2018.1.163/linux//compiler/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/zlib/1.2.11/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/generic/numactl/2.0.11/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/libxml2/2.9.7/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/hwloc/1.11.9/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/openmpi/3.0.0/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/szip/2.1.1/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/hdf5/1.8.18/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/pnetcdf/1.8.1/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/netcdf/4.6.0/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/flook/0.7.0/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/parmetis/4.0.3/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/scotch/6.0.4/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/mumps/5.1.2/intel-18.0.1/include -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/fftw/3.3.7/intel-18.0.1/include

MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=.

FPPFLAGS += -DSIESTA__METIS -DSIESTA__MUMPS -DTS_NOCHECKS
ADDLIB += -lzmumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis
METIS_LIB = -lmetis
FFTW_PATH = /zdata/groups/common/nicpa/2018-feb/XeonX5550/fftw/3.3.7/intel-18.0.1
FFTW_INCFLAGS = -I$(FFTW_PATH)/include
FFTW_LIBS = -L$(FFTW_PATH)/lib -lfftw3 $(METIS_LIB)
LIBS += $(METIS_LIB)
FPPFLAGS += -DNCDF -DNCDF_4 -DNCDF_PARALLEL
COMP_LIBS += libncdf.a libfdict.a
FPPFLAGS += -DSIESTA__FLOOK
FLOOK_LIB = -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/flook/0.7.0/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/flook/0.7.0/intel-18.0.1/lib -lflookall -ldl
INCFLAGS += -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/flook/0.7.0/intel-18.0.1/include
LIBS += $(FLOOK_LIB)

FPPFLAGS += -DSIESTA__ELPA
ELPA_LIB = -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/elpa/2017.05.003/intel-18.0.1/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/elpa/2017.05.003/intel-18.0.1/lib -lelpa
INCFLAGS += -I/zdata/groups/common/nicpa/2018-feb/XeonX5550/elpa/2017.05.003/intel-18.0.1/include/elpa
LIBS += $(ELPA_LIB)

FPPFLAGS += -DSIESTA__MRRR

.F.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $<
.F90.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $<
.f.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $<
.c.o:
 $(CC) -c $(CFLAGS) $(INCFLAGS) $(FPPFLAGS) $<
.f90.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $<

atom.o: atom.F
 $(FC) -c -O1 $(INCFLAGS) $(FPPFLAGS) $<

m_new_dm.o: m_new_dm.F90
 $(FC) -c -O2 $(INCFLAGS) $(FPPFLAGS) $<

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