Mint build

Qbox installation issues
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mgoldey
Posts: 14
Joined: Tue Sep 23, 2014 10:26 pm

Mint build

Post by mgoldey »

I could use a hand sorting out what is going wrong with my build here.

I built and linked using the makefile at end, but the resulting executable does not work. Should be a trivial fix, but I don't understand how I'm linking against a dynamic library for pthreads, and I can't find a static one.

Error is as follows

Code: Select all

[qbox] <cmd>species oxygen O_HSCV_PBE-1.0.xml</cmd>
  SpeciesCmd: defining species oxygen as O_HSCV_PBE-1.0.xml
*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x8
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f1fb5b30340]
[ 1] ../../src/qb() [0x4319c0]
[ 2] ../../src/qb() [0x42a5a9]
[ 3] ../../src/qb() [0x47d292]
[ 4] ../../src/qb() [0x479ec2]
[ 5] ../../src/qb() [0x414f3d]
[ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f1fb43f9ec5]
[ 7] ../../src/qb() [0x415fdf]
*** End of error message ***
XERCES, FFTW, LAPACK, SCALAPACK, BLACS installed via apt-get in Linux Mint, Intel MKL included, mpicxx references gnu compilers

Code: Select all

PLTOBJECTS = readTSC.o

CXX = mpicxx
LD = mpicxx

PLTFLAGS = -DUSE_MPI -DSCALAPACK -DADD_
PLTFLAGS += -DUSE_XERCES
PLTFLAGS += -DUSE_FFTW -DPTHREAD
PLTFLAGS += -D_LARGEFILE64_SOURCE  -D_FILE_OFFSET_BITS=64 -DAPP_NO_THREADS -DXML_USE_NO_THREADS

INCLUDE = -I/usr/include

CXXFLAGS= -O3 $(INCLUDE) $(PLTFLAGS) $(DFLAGS) -g -openmp  -pthread

LDFLAGS = $(LIBPATH) $(LIBS) -g
LIBPATH =

LIBS =  -Bstatic -L$(MKLROOT)/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64  \
         -lmkl_sequential -lmkl_core -lmkl_blacs_openmpi_lp64   \
         -lmkl_lapack95_lp64 -lm -lpthread -static-libgcc \
         -lfftw \
         -lxerces-c -luuid
Last edited by mgoldey on Wed Sep 24, 2014 3:16 am, edited 1 time in total.
mgoldey
Posts: 14
Joined: Tue Sep 23, 2014 10:26 pm

Re: Mint build

Post by mgoldey »

GDB has isolated where this is occurring.

Code: Select all

Program received signal SIGSEGV, Segmentation fault.
Species::initialize (this=this@entry=0xa56580, rcpsval=rcpsval@entry=1.5) at Species.C:65
65	  const int np = vps_[0].size();
fgygi
Site Admin
Posts: 139
Joined: Tue Jun 17, 2008 7:03 pm

Re: Mint build

Post by fgygi »

A few questions:
Which version of Xerces-C does apt-get install?
Is it essential to make a static build?
Is the Intel compiler available on that platform?
mgoldey
Posts: 14
Joined: Tue Sep 23, 2014 10:26 pm

Re: Mint build

Post by mgoldey »

fgygi wrote:A few questions:
Which version of Xerces-C does apt-get install?
Is it essential to make a static build?
Is the Intel compiler available on that platform?
It's Xerces-C 3.1
No, dynamic should be fine.
Intel compilers are available.
fgygi
Site Admin
Posts: 139
Joined: Tue Jun 17, 2008 7:03 pm

Re: Mint build

Post by fgygi »

Try to add the following macro definition to the makefile:

Code: Select all

-DXERCESC_3
mgoldey
Posts: 14
Joined: Tue Sep 23, 2014 10:26 pm

Re: Mint build

Post by mgoldey »

Solution found:
Using intel compilers, with fftw as installed by apt-get
XERCES-C 2.8 compiled under $XERCESCROOT
using

Code: Select all

cd $XERCESCROOT/src/xercesc
./runConfigure -plinux -cicc -xicpc -minmem -nsocket -tnative -rpthread -l-m64 -z-m64 -b64 -s
Adding to .bashrc

Code: Select all

export XERCESCROOT=$HOME/Programs/xerces-c-src_2_8_0
export OMPI_CC=icc
export OMPI_CXX=icpc
Makefile is

Code: Select all

 PLTOBJECTS = readTSC.o

 XERCESCDIR = $(XERCESCROOT)
 FFTWDIR =/usr

 CXX=mpicxx
 LD=$(CXX)

 OPT = -O3  -ipo
 OMP = -openmp

 PLTFLAGS += $(OPT) $(OMP) -DIA32 -DUSE_FFTW -D_LARGEFILE_SOURCE \
           -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DSCALAPACK -DADD_ \
           -DAPP_NO_THREADS -DXML_USE_NO_THREADS -DUSE_XERCES \
           -DMPICH_IGNORE_CXX_SEEK

 INCLUDE = -I$(FFTWDIR)/include -I$(XERCESCDIR)/include

 CXXFLAGS= -D$(PLT) $(INCLUDE) $(PLTFLAGS) $(DFLAGS)

 LIBPATH = -L$(XERCESCDIR)/lib -L$(FFTWDIR)/lib  -L$(MKLROOT)/lib/intel64

 LIBS =  $(OMP) -lxerces-c  -lfftw \
         -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core \
         -lmkl_intel_thread -lmkl_blacs_openmpi_lp64 -lpthread -lm

 LDFLAGS = $(LIBPATH) $(LIBS)
mgoldey
Posts: 14
Joined: Tue Sep 23, 2014 10:26 pm

Re: Mint build

Post by mgoldey »

Updated for 1.60.4, change -DUSE_FFTW to -DUSE_FFTW3

Code: Select all

 PLTOBJECTS = readTSC.o

 XERCESCDIR = $(XERCESCROOT)
 FFTWDIR =/usr

 CXX=mpicxx
 LD=$(CXX)

 OPT = -O3  -ipo
 OMP = -openmp

 PLTFLAGS += $(OPT) $(OMP) -DIA32 -DUSE_FFTW3 -D_LARGEFILE_SOURCE \
           -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DSCALAPACK -DADD_ \
           -DAPP_NO_THREADS -DXML_USE_NO_THREADS -DUSE_XERCES \
           -DMPICH_IGNORE_CXX_SEEK

 INCLUDE = -I$(FFTWDIR)/include -I$(XERCESCDIR)/include

 CXXFLAGS= -D$(PLT) $(INCLUDE) $(PLTFLAGS) $(DFLAGS)

 LIBPATH = -L$(XERCESCDIR)/lib -L$(FFTWDIR)/lib  -L$(MKLROOT)/lib/intel64

 LIBS =  $(OMP) -lxerces-c  -lfftw \
         -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core \
         -lmkl_intel_thread -lmkl_blacs_openmpi_lp64 -lpthread -lm

 LDFLAGS = $(LIBPATH) $(LIBS)
mgoldey
Posts: 14
Joined: Tue Sep 23, 2014 10:26 pm

Re: Mint build

Post by mgoldey »

Updated for 1.62.3, intel 16.0.0.

I ran into some odd conflicts between intelmpi and openmpi, primarily in linking and running (MKL couldn't find the MPI libraries necessary). Embarrassingly, I am unsure quite how I resolved these conflicts, but the following Makefile compiles, links, and runs fine.

Code: Select all

 PLTOBJECTS = readTSC.o

 XERCESCDIR = $(XERCESCROOT)
 FFTWDIR =/opt/fftw3
 MPIDIR=/opt/openmpi
 CXX=mpicxx
 LD=$(CXX)


 OPT = -O3  
 OMP = -qopenmp -liomp5

 PLTFLAGS += $(OPT) $(OMP) -DIA32 -DUSE_FFTW3 -D_LARGEFILE_SOURCE \
           -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DSCALAPACK -DADD_ \
           -DAPP_NO_THREADS -DXML_USE_NO_THREADS -DUSE_XERCES \
           -DMPICH_IGNORE_CXX_SEEK

 INCLUDE = -I$(FFTWDIR)/include -I$(XERCESCDIR)/include -I${MKLROOT}/include

 CXXFLAGS= -D$(PLT) $(INCLUDE) $(PLTFLAGS) $(DFLAGS)

 LIBPATH = -L$(XERCESCDIR)/lib -L$(FFTWDIR)/lib  -L$(MKLROOT)/lib/intel64 -L$(MPIDIR)/lib

 LIBS =  $(OMP) -lxerces-c  -lfftw3  \
		 -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 \
		 -lmkl_cdft_core -lmkl_intel_lp64 -lmkl_core \
		 -lmkl_intel_thread -lmkl_blacs_intelmpi_lp64 -lpthread -lm         
 LDFLAGS = $(LIBPATH) $(LIBS)
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