Installing cpseis on Centos 7

[bachir]

Dear All,
Anyone tried to install CPSEIS on centos 7 , if yes , is there any help
please
thanks much
Bachir

[bme...@hpcsociety.org]

I'm working on it, but have not finished. I'll post any changes needed when I encounter and make updates.

Bill Menger
HPC Consultant
bme...@hpcsociety.org
281-633-6820

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[Bjorn_Miese]

I assume you have installed CPSeis before in Centos 5/6 or some other

enterprise linux, and know how to setup .bashrc, cps_config.dat and so on.

You need the "everything" ISO (burnt to dual-layer DVD).

I presume Scientific Linux will work as well, but Springdale and

Oracle linux have smaller ISOs, and I don't know what they left out.

Install Centos 7 with 'development and creative workstation' option.

 Further select these extras:

Additional development

Compatibility libraries

Development tools

Legacy X window system compatibility

 After installation, you also need:

yum install libstdc++.i686

yum install libstdc++-static

yum install xterm

yum install xorg-x11-fonts-ISO8859-1*

Install Sun/Oracle JDK version 6u45

Install Intel compiler version 13 or later.

Get the latest revision of CPSEIS from sourceforge.

Build FFTW

For MPICH2, edit build_mpich2.sh

change "-fno-second-underscore" to "-assume no2underscores" in FFLAGS

add a line "CXX=icps"

Locate the directory containing "libsvml.a" in your Intel compiler installation.

Then in your cpseis directory, create a symbolic link named "intel_x86_64"

to that directory.

Edit makefile.spws

Replace libguide and libguide_stats with libiomp5 (this changed in Intel

compiler version 12).

Change INCDIRS to remove "X11R6" between usr and include (these paths do

occasionally change between linux versions).

Rename the file hh7.f to hh7.foff otherwise va will not build.  There are

multiple definition of symbols from both headgeth.o and hh7.o (from the

Fortran 77 files in utlib directory). This is a weird problem that I did

not encounter before.  Anyway renaming hh7.f made it go away.

For platform makefile in wrappers/etc, can copy makefile.x86_64_intel91_mpich2

For platform makefile in spws_home/making, FOR_LIBS and INCDIRS have to be

customised for each major version of linux. So it should look like this:

#<CPS_v1 type="SCRIPT" pretag="#"/>

##-------------------------- x86_64_intel13_mpich2 -------------------------------##

# -------------------------------for RHEL 7 and Intel 13

# using g++ instead of icpc, otherwise program cfg does not work

permitted_architectures = x86_64

permitted_hosts          = unrestricted

FC         = mpif90 -c -g

FC_LINK    = mpif90 -g

CC         = mpicc -c -g -Wall -fPIC -mcmodel=medium \

                 -DLINUX -DLINUXI -D_REENTRANT -D_FILE_OFFSET_BITS=64 \

                                             -DIA64 -D_64LINUXI91

CC_LINK    = mpicc

CXX        = g++ -c -g -Wall -fPIC -mcmodel=medium \

                -DLINUX -DLINUXI -D_FILE_OFFSET_BITS=64 \

                                             -DIA64 -D_64LINUXI91

CXX_LINK   = mpif90 -g -cxxlib -nofor_main -i-static

CXX_DEPEND = icpc -MM -DLINUX -DLINUXI -D_FILE_OFFSET_BITS=64

AR_LINK    = ar -ursv

SO_LINK    = mpicc -shared -g

MODEXT     = .mod

MODFLAG    = -I

FOR_LIBS   =  /lib/gcc/x86_64-redhat-linux/4.8.2/libstdc++.a -liomp5

GUI_LIBS    = -L/usr/lib64 -lXm -lXmu -lXp -lXext -lXt -lSM -lICE -lX11

MATH_LIBS = -lm -lpthread -lc

JAVA_LIBS = -L$(JAVA_HOME)/jre/lib/amd64 -L$(JAVA_HOME)/jre/lib/amd64/server \

            -ljava -ljvm -lverify

INCDIRS += $(JAVA_HOME)/include $(JAVA_HOME)/include/linux

INCDIRS += /usr/include

INCDIRS += /usr/include/X11

INCDIRS += /usr/include/Xm

INCDIRS += /usr/include/X11/Xmu

INCDIRS += /usr/include/X11/extensions

INCDIRS += /usr/include/X11/SM

INCDIRS += /usr/include/X11/ICE

INCDIRS += /usr/include/X11/Xaw

[Bill Menger (gmail)]

Thanks so much for that guide to CentOS7.  It is very good.  There is one small typo,

change:

                    add a line "CXX=icps"

to:
                    add a line "CXX=icpc"

Bill

[Bachir]

Dear all,

Please would anyone check my install_log file attached in the email.

I am installing Cpseis on centos 7 Linux nexus 4.14.8-1.el7.elrepo.x86_64 #1 SMP Wed Dec 20 16:06:25 EST 2017 x86_64 x86_64 x86_64 GNU/Linux

together with intel compiler icc version 15.0.3 (gcc version 4.8.5 compatibility.

Java completed as on normal, build mpich2 completed , but ended with the following message (tail of the install_cpseis.log) , see bellow

Is there any guide and help please 

Thanks much 

Bachir 

make[6]: Leaving directory `/apps/thirdparty/mpich2-1.1/src/pm/util'

icc -fPIC -O -O2  -static  -o pmi_proxy pmi_proxy.o \

pmi_proxy_utils.o pmi_proxy_cb.o  -L../../lib -lhydra -L../../../util \

-lmpiexec -L../../../../../lib -lmpich -lpthread  -lpthread    -lrt    

ld: cannot find -lpthread

ld: cannot find -lpthread

ld: cannot find -lrt

ld: cannot find -lm

ld: cannot find -lc

ld: cannot find -ldl

ld: cannot find -lc

make[5]: *** [pmi_proxy] Error 1

make[5]: Leaving directory `/apps/thirdparty/mpich2-1.1/src/pm/hydra/pm/pmiserv'

make[4]: *** [all-redirect] Error 1

make[4]: Leaving directory `/apps/thirdparty/mpich2-1.1/src/pm/hydra/pm'

make[3]: *** [all-redirect] Error 2

make[3]: Leaving directory `/apps/thirdparty/mpich2-1.1/src/pm/hydra'

make[2]: *** [all-redirect] Error 1

make[2]: Leaving directory `/apps/thirdparty/mpich2-1.1/src/pm'

make[1]: *** [all-redirect] Error 2

make[1]: Leaving directory `/apps/thirdparty/mpich2-1.1/src'

make: *** [all-redirect] Error 2

libtoolize: You should add the contents of the following files to `aclocal.m4':

libtoolize:   `/usr/share/aclocal/libtool.m4'

libtoolize:   `/usr/share/aclocal/ltoptions.m4'

libtoolize:   `/usr/share/aclocal/ltversion.m4'

libtoolize:   `/usr/share/aclocal/ltsugar.m4'

libtoolize:   `/usr/share/aclocal/lt~obsolete.m4'

libtoolize: Remember to add `LT_INIT' to configure.in.

libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and

libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.

libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.

Build mpich2 complete. Add /apps/thirdparty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2/bin to your path.

Error running build_mpich2.sh script

Error detected.  Hit return to exit

[Bill Menger]

These warnings in the build for mpich2 don't look good.  I'll try to run a close "clone" of what you are doing on my machine that is at CentOS7.4 (but I don't have intel compilers) and see how i need to modify the script called "build_mpich2.sh" in the scripts directory of cpseis.  That is where the error is coming from.

configure: WARNING: Unrecognized options: --enable-threads, --enable-sharedlibs, --enable-f77, --enable-f90, --enable-cxx, --enable-static, --with-atomic-primitives

Bill

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Bill Menger

Houston HPC Services, Inc.
(281) 633-6820

[Pedro Valdez]

Towards the end of install_cpseis.log, before the error you have this:

icc -fPIC -O -O2  -static  -o pmi_proxy pmi_proxy.o \
pmi_proxy_utils.o pmi_proxy_cb.o  -L../../lib -lhydra -L../../../util \
-lmpiexec -L../../../../../lib -lmpich -lpthread  -lpthread    -lrt

it is looking for the libpthread et cetera 5 levels above the current sudirectory, which is more than that below root.
libpthread is in /lib and /usr/lib
I didn't use the install script, but did all the steps individually. I always built mpich2 version 1.2.1p1 instead of 1.1
I had a look at the build output from that and it doesn't have the "-L../.../.../.../.." so finds the libraries in their natual locations.

So perhaps try building 1.2.1p1 first, Edit the build_mpich2.sh script and change
PRODUCT=mpich2-1.2.1p1

 then the install script should find mpd it will carry on to make CPSEIS.

[Bill Menger]

Try Pedro's change first, it will likely work if you change the product to the one he suggests.

Bill

[Halitim Bachir]

I build mpich2 separately then linked as on the HOW_TO_MAKE_CPSEIS, the    install_cpseis script  using gfortran  run as on normal but i had  diffrent message as on the attached log file.

This is the tail of the install_cpseis script 

====================

making vpick_superwrap.o

mpif90 -c -g -fPIC -fno-range-check -ffree-form -ffree-line-length-none -DLINUX -DLINUXI -I. -I/include /apps/cpseis/src/vpick_superwrap.f90 -o vpick_superwrap.o

ifort: command line warning #10006: ignoring unknown option '-fno-range-check'

ifort: command line warning #10006: ignoring unknown option '-ffree-form'

ifort: command line warning #10006: ignoring unknown option '-ffree-line-length-none'

making vtrin.o

mpif90 -c -g -fPIC -fno-range-check -ffree-form -ffree-line-length-none -DLINUX -DLINUXI -I. -I/include /apps/cpseis/src/vtrin.f90 -o vtrin.o

ifort: command line warning #10006: ignoring unknown option '-fno-range-check'

ifort: command line warning #10006: ignoring unknown option '-ffree-form'

ifort: command line warning #10006: ignoring unknown option '-ffree-line-length-none'

making vtrin_superwrap.o

mpif90 -c -g -fPIC -fno-range-check -ffree-form -ffree-line-length-none -DLINUX -DLINUXI -I. -I/include /apps/cpseis/src/vtrin_superwrap.f90 -o vtrin_superwrap.o

ifort: command line warning #10006: ignoring unknown option '-fno-range-check'

ifort: command line warning #10006: ignoring unknown option '-ffree-form'

ifort: command line warning #10006: ignoring unknown option '-ffree-line-length-none'

making libcps.so

mpif90 -shared -g -fPIC -O2 -DLINUX -DLINUXI -DNEED_UNDERSCORE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/apps/cpseis/include -DLINUXGCC -o /apps/cpseis/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libcps.so adpsub_crou.o apin_crou.o avocorr_crou.o bfio.o binary_search.o cb.o cgetsys.o cio_crou.o cmem_crou.o cnfg_crou.o cps_crou.o cpsacct.o cpslog.o cputsys.o cterp.o cube.o dbug_crou.o exptilde_crou.o filebox_crou.o finquire_crou.o gpi_crou.o ibsma_crou.o inquire.o int_api_crou.o lbo_crou.o lnklst_crou.o memman_crou.o memory.o mth_crou.o mtio.o mutefile.o pcps_crou.o pcpsx_crou.o pfio.o ppavo_crou.o qsearch.o readcard.o rice.o segy_crou.o sizeof_crou.o skio.o str.o string_crou.o superproc_crou.o superwrap.o swap.o tapeio.o tcclient.o tfatt_crou.o tpioclnt.o tpiocnfg.o tredfile.o tredit_crou.o truevalue.o ttrin_crou.o ttrot_crou.o txfr_crou.o unix_crou.o workstation.o wrdc_crou.o xdim.o xydim.o xyzdim.o cfeutil_crou.o cfe_util_crou.o abal.o abal_superwrap.o abra.o abra_superwrap.o abrakadabra.o acorr.o acorr_superwrap.o addext.o adns.o adns_superwrap.o adpsub.o adpsub_superwrap.o alamo.o alamo_superwrap.o alphasort.o ameq.o amod.o ampdg.o ampdg_superwrap.o ap1.o apin.o apin_superwrap.o array.o atblk.o atrin.o atrin_superwrap.o atrot.o atrot_superwrap.o avagrad.o avagrad_superwrap.o avast.o avast_superwrap.o avoans.o avoans_superwrap.o avocorr.o avocorr_superwrap.o avonrm.o avonrm_superwrap.o avopcomp.o avopcomp_superwrap.o avosts.o avosts_superwrap.o avovan.o avovan_superwrap.o avovit.o avovit_superwrap.o awindow.o awindowlist.o bandps.o basetrace.o bavel.o binsort.o buhci.o buildlist.o bunch.o bunch_superwrap.o c4we.o c4we_superwrap.o cardset.o cardsetlist.o cc3d.o cc3d_superwrap.o cfds.o cfds_superwrap.o pclun.o chart.o chart_superwrap.o cio.o clean.o cleanup.o cleanup_superwrap.o clip.o clip_superwrap.o cmem.o cmpi.o cnearts.o cnearts_superwrap.o cnfg.o codmo.o codmo_superwrap.o color.o color_superwrap.o colrplot.o combine.o combine_superwrap.o comp.o comp_superwrap.o conjgrad.o convert.o cordip.o cps.o cpsio.o cpsplot.o cpssig.o cpucount.o csvd.o ctan.o ctan_superwrap.o cubeterp.o cuhci.o cvptom.o dabra.o dabra_superwrap.o datacards.o datumgrid.o dbgain.o dbgain_superwrap.o dbritr.o dbug.o decon.o decon_superwrap.o densify.o dio.o dist.o dist_superwrap.o dmap3d.o dmap3d_superwrap.o dmo3d.o dmo3d_superwrap.o dmoprep.o dmoprep_superwrap.o dooskip.o drc.o drc_superwrap.o dsig.o dsig_superwrap.o dyncc.o dynsamp.o eagc.o eagc_superwrap.o eda.o eda3d.o eda3d_superwrap.o eda_superwrap.o elev.o elev_superwrap.o eureka.o exo.o exo_superwrap.o exptilde.o extsize.o ezcheck.o ezcheck_superwrap.o fbal.o fbal_superwrap.o ffava.o ffava_superwrap.o fft.o fftf77.o fgd.o fgd_superwrap.o fgdrev.o fgdrev_superwrap.o filebox.o fill.o fill_superwrap.o filtiir.o filtiir_superwrap.o filtp.o filtp_superwrap.o finquire.o fio.o fioutil.o fish.o fish_superwrap.o fkap.o fkap_superwrap.o fkfilt.o fkfilt_superwrap.o fkinterp.o fkinterp_superwrap.o fktmig.o fktmig_superwrap.o fktr.o fktr_superwrap.o flexbin.o flexbin_superwrap.o flexio.o floatio.o floatio_frou.o fltr.o foursort.o fxcard.o fxdata.o fxdecon.o fxdecon_superwrap.o fxdnoise.o fxdnoise_superwrap.o fxinterp.o fxinterp_superwrap.o fxpar.o gather.o gather_superwrap.o gathr.o gausselim.o gdiv.o gdiv_superwrap.o genfilt.o genfilt_superwrap.o geomdata.o geomio.o geomio1.o geomio2.o geomio_frou.o getlun.o getsys.o gpi.o gplot.o grab.o grab_superwrap.o grid.o grid_frou.o gridcheck.o gridlib.o gridlib_frou.o gstack.o gstack_superwrap.o gstk.o gstk_superwrap.o gvs.o gvs_superwrap.o hashlist.o headcheck.o headcheck_superwrap.o headfit.o headfit_superwrap.o headmap.o headmap_superwrap.o headsave.o headsum.o headsum_superwrap.o headswap.o headswap_superwrap.o hist.o histogram.o histprim.o hrzpck.o hrzstk.o hrzstk_superwrap.o hsyn.o hsyn_superwrap.o hsynmod.o hsynmod_superwrap.o hvel.o hvel_superwrap.o ibsma.o ibsma_superwrap.o ims.o ims_superwrap.o incutils.o interp.o increment.o integrate.o integrate_superwrap.o interpolate.o intpvelf.o incjobname.o int_api.o iq.o iq_superwrap.o job_data.o job_data_superwrap.o ka.o ka_superwrap.o kadabra.o kastats.o kastats_superwrap.o kcpu.o kdmo.o kdmo_superwrap.o kfun.o latwin.o lav.o lbo.o least.o linterp.o ll.o lnklst.o madc.o madc_superwrap.o manhist.o mapsegy.o masker.o masker_superwrap.o matfun.o mdip.o mdip_superwrap.o mds.o mds_superwrap.o median.o mem.o memfun.o memman.o mfile.o mfilebox.o mfrs.o mfrs_superwrap.o mgather.o mgather3d.o mgd.o mgd_superwrap.o migfun.o mix.o mix_superwrap.o model.o modgmem.o modgrid.o modgrid_frou.o modmo.o modmo2d.o modmo2d_superwrap.o modmo_superwrap.o modspec.o moveout.o mtfun.o mtfun_superwrap.o mth.o multgather.o multwin.o mute.o mute_superwrap.o mutehw.o muteio.o muteio1.o muteio2.o mvxp.o mvxp_superwrap.o mzpc.o mzpc_superwrap.o named_constants.o nmo.o nmo_superwrap.o nmoprim.o norm.o norm_superwrap.o nthcol.o off2ang.o off2ang_superwrap.o onesort.o opfilt.o pairmerge.o pairmerge_superwrap.o parameter.o pario.o parlist.o path.o pathcheck.o pathchoose.o pattern.o pc.o pc_frou.o pcps.o pcpsx.o permtfile.o permtset.o pfilt3c.o pfilt3c_superwrap.o pgps.o pgps_superwrap.o ph2off.o ph2off_superwrap.o pickio.o pickset.o pickset_superwrap.o pjar.o pjar_frou.o pkutil.o polyfit.o pp.o ppavo.o ppio.o prnfun.o process.o project_data.o project_data_superwrap.o pstmig.o pstmig_superwrap.o putsys.o qest.o qest_superwrap.o randgth.o randgth_superwrap.o ranline.o ranline_superwrap.o rantfile.o rcpfile.o rcpout.o rcpout_superwrap.o rcsum.o reg.o reg2d.o reg2d_superwrap.o reg_superwrap.o regbin.o regbin_superwrap.o res.o res_superwrap.o resth.o resth_superwrap.o rfab.o rfab_superwrap.o rmul.o rmul_superwrap.o rnsyn.o rnsyn_superwrap.o rollalong.o rollingbins.o rsvd.o rtc.o rtc_superwrap.o rtcstatio.o scab.o scab_superwrap.o scale.o scale_superwrap.o scdecon.o scdecon_superwrap.o sdip.o sdip_superwrap.o sdiputil.o segy.o seldmo.o seldmo_superwrap.o select.o select_superwrap.o semdip.o sequence.o setmute.o setmute_superwrap.o setpoly.o setpoly_superwrap.o setword.o setword_superwrap.o shft.o shft_superwrap.o singletracesupport.o sio.o sisc.o sisc_superwrap.o sizeof.o slab.o slab_superwrap.o slice.o slice_superwrap.o slicer.o slicer_superwrap.o slst.o slst_superwrap.o snrm2.o sort.o sortkeys.o spct.o spct_superwrap.o spike.o spike_superwrap.o txinterp.o txinterp_superwrap.o spline.o splt.o splt_superwrap.o spsrps.o spsrps_superwrap.o spti.o spti_superwrap.o statcc.o statclass.o statclasses.o statfile.o stathelper.o statio.o statio1.o statio2.o statio_frou.o statistics.o statshift.o statutil.o statutil_frou.o stk.o stk_superwrap.o stkscale.o stretch.o stretch_superwrap.o string.o stringlist.o superproc.o superproc_frou.o surfacegrid.o sva.o sva_superwrap.o swap_frou.o synbp.o synbp_superwrap.o syngrid.o synref.o synvofz.o tablesave.o tablesave_superwrap.o tablesort.o tablesort_superwrap.o taper.o tcatclient.o tdc.o tdc_superwrap.o tdfilter.o tdmp.o tdmp_superwrap.o telav.o telav_superwrap.o tempname.o temptcache.o temptfile.o terputil.o tfatt.o tfatt_superwrap.o tftable.o timecheck.o timeglob.o time.o timer.o timesel.o timezero.o tpick.o tpick_superwrap.o tpow.o tpow_superwrap.o traceterp3d.o traceterp3d_superwrap.o trbuf.o trcio.o trciof77.o trciof77wrapper.o tredit.o tredit_superwrap.o trin.o trin_superwrap.o trinsort.o trinsort_superwrap.o triplemerge.o triplesort.o trmo.o trmo_superwrap.o trot.o trot_superwrap.o trscan.o trstats.o trstats_superwrap.o tsel.o tsel_superwrap.o tslc.o tslc_superwrap.o tslice.o tslice_superwrap.o tsmute.o tsmute_superwrap.o parallelsort.o parallelsort_superwrap.o tsort.o tsort_superwrap.o tsortparams.o tmerge.o tsvf.o tsvf_superwrap.o ttmo.o ttmo_superwrap.o ttrin.o ttrin_superwrap.o ttrot.o ttrot_superwrap.o tvf.o tvf_superwrap.o tweights.o txfr.o ungather.o ungather_superwrap.o unix.o utel.o utel_superwrap.o valuedump.o valuedump_superwrap.o vc.o vc_superwrap.o veledit.o veledit_superwrap.o velfile.o velfun.o velgrid.o velio.o velio1.o velio2.o velio3.o velio4.o velio_frou.o velset.o velterp.o velutil.o vpick.o vpick_superwrap.o vtrim.o vtrim_superwrap.o vtrimmer.o vtrin.o vtrin_superwrap.o wavelet.o workfile.o worklist.o wrdc.o wsep.o wsep_superwrap.o xp.o xps_superwrap.o xps.o xp_superwrap.o xputil.o zoeppritz.o buildjob.o cfegui.o cfelist.o cfeprocess.o cfebuildlist.o cfelistbuffer.o cfesj.o cfe.o cfesl.o cfemwb.o cfewb.o cfemenu.o cfejava.o cfestruct.o cfewindow.o cfeutil.o cfesub_frou.o cfebld_frou.o -L/apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib -lfftw -lrfftw -L/lib -lmpich -lfmpich  -lm -lutil -lpthread

ld: /usr/local/lib/libfftw.a(planner.o): relocation R_X86_64_32 against `fftw_config' can not be used when making a shared object; recompile with -fPIC

/usr/local/lib/libfftw.a: error adding symbols: Bad value

make: *** [/apps/cpseis/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libcps.so] Error 1

PATH is not set up to find your installation of CPSeis front end, cfe.

PATH is not set up to find your installation of CPSeis icps.

There are 2 error(s) in your setup.

Error detected.  Hit return to exit

 

[Bill Menger]

Near the end, you have an error (repeated below)

ld: /usr/local/lib/libfftw.a(planner.o): relocation R_X86_64_32 against `fftw_config' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libfftw.a: error adding symbols: Bad value
make: *** [/apps/cpseis/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libcps.so] Error 1

This indicates that fftw is not coming from $THIRDPARTY_DIR/fftw but instead is from /usr/local/lib.  The build for that static library was done without -fPIC (or there was no shared libfftw.so created) and so the objects will not link into libcps.so.

For cfe to work, libcps.so must be created.

The best thing to try is to run the $CPSEIS_INSTALL_DIR/scripts/build_fftw.sh script.  You will need to remove the hidden file ".built_fftw" in the $THIRDPARTY_DIR and run the script.  Then I think you should be able to get to the next step.

If all builds, but still no cfe, try the following:

(assuming icps works first! -- try it by typing: "icps".  You should get an error saying you need to supply a work file.  )

Go to the $CPSEIS_INSTALL_DIR/platforms/$CPSEIS_ARCH directory and type "make cfe"

Sorry for the short and insufficient help.  Keep the questions coming, and as I can, I'll make the install scripts more robust.

Bill

[Halitim Bachir]

I rebuilt fftw using the build script from $CPSEIS_HOME/scripts , then  build_mpich using mpich2-1.2.1p1  by  changing PRODUCT=mpich2-1.2.1p1  then make depend , makee all

the installation went up to icps and stopped with the following message.

ldd -r /apps/cpseis/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libcps.so

        linux-vdso.so.1 =>  (0x00007ffeb878b000)

        librt.so.1 => /lib64/librt.so.1 (0x00007f4f678a4000)

        libfftw.so.2 => /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libfftw.so.2 (0x00007f4f6766e000)

        librfftw.so.2 => /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/librfftw.so.2 (0x00007f4f6743f000)

        libmpich.so.1.2 => /apps/thirdparty/mpich2-1.2.1p1/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libmpich.so.1.2 (0x00007f4f6707b000)

        libfmpich.so.1.2 => /apps/thirdparty/mpich2-1.2.1p1/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libfmpich.so.1.2 (0x00007f4f66e5b000)

        libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f4f66b39000)

        libm.so.6 => /lib64/libm.so.6 (0x00007f4f66836000)

        libutil.so.1 => /lib64/libutil.so.1 (0x00007f4f66633000)

        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f4f66417000)

        libmpichf90.so.1.2 => /apps/thirdparty/mpich2-1.2.1p1/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libmpichf90.so.1.2 (0x00007f4f66213000)

        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f4f65ffd000)

        libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f4f65dc1000)

        libc.so.6 => /lib64/libc.so.6 (0x00007f4f659fd000)

        /lib64/ld-linux-x86-64.so.2 (0x0000560f3e812000)

making libcgm.so

mpif90 -shared -o /apps/cpseis/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libcgm.so pip_trace.o cgm_c.o cgmsubs.o circle.o colorcgm.o fillcgm.o init.o line.o marker.o raster.o set_defaults.o text.o trans.o cgm.o -L/apps/thirdparty/f

ftw-2.1.5/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib -lfftw -lrfftw -L/lib -lmpich -lfmpich  -lm -lutil -lpthread

ldd -r /apps/cpseis/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libcgm.so

        linux-vdso.so.1 =>  (0x00007ffcbae89000)

        librt.so.1 => /lib64/librt.so.1 (0x00007f55639de000)

        libfftw.so.2 => /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libfftw.so.2 (0x00007f55637a8000)

        librfftw.so.2 => /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/librfftw.so.2 (0x00007f5563579000)

        libmpich.so.1.2 => /apps/thirdparty/mpich2-1.2.1p1/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libmpich.so.1.2 (0x00007f55631b5000)

        libfmpich.so.1.2 => /apps/thirdparty/mpich2-1.2.1p1/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libfmpich.so.1.2 (0x00007f5562f95000)

        libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f5562c73000)

        libm.so.6 => /lib64/libm.so.6 (0x00007f5562970000)

        libutil.so.1 => /lib64/libutil.so.1 (0x00007f556276d000)

        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5562551000)

        libmpichf90.so.1.2 => /apps/thirdparty/mpich2-1.2.1p1/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libmpichf90.so.1.2 (0x00007f556234d000)

        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f5562137000)

        libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f5561efb000)

        libc.so.6 => /lib64/libc.so.6 (0x00007f5561b37000)

        /lib64/ld-linux-x86-64.so.2 (0x0000561338da3000)

making icps

mpif90 -g -fPIC -fno-range-check -ffree-form -ffree-line-length-none -DLINUX -DLINUXI -I. -I/include -o /apps/cpseis/platforms/Linux_x86_64_2.17_gfortran_mpich2/bin/icps                 icps.o engine.o   /apps/cpseis/platforms/Linux_x86_

64_2.17_gfortran_mpich2/lib/libcps.a /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/libfftw.a /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib/librfftw.a /lib/libmpich.a /lib/libfmp

ich.a  -lutil -lm

gfortran: error: /lib/libmpich.a: No such file or directory

gfortran: error: /lib/libfmpich.a: No such file or directory

make: *** [icps] Error 1

 

 

[Bill Menger]

It looks like the make is looking for static mpich libraries in a default location, not from thirdparty area.

/lib/libmpich.a and /lib/libfmpich.a should be located (on your build) in this directory:

/apps/thirdparty/mpich2-1.2.1p1/platforms/Linux_x86_64_2.17_gfortran_mpich2/lib

I'm working on the build for CentOS7.4 now, and running a new version of mpich2 called mpich-3.2.1.  It is in the process of building, I don't know if it will succeed yet.  The old version (1.1) was ok for CentOS6.4, but I was able to replicate your build errors exactly when attempting it on CentOS7.4.

See if there are libmpich.a and libfmpich.a files located in the above directory and if so, you may be missing an environment variable.  I can't tell.

If they exist, then I will know where to start looking for the error.  Hopefully I'll have a better build script soon, with a more up to date version of mpich.

You can also build with openmpi if you want to.  There is a script to build it instead of mpich if you want.

Bill

[Halitim Bachir]

I have both of them located at /apps/thirdparty/mpich2-1.2.1p1/lib,

i will try openmpi at the same time

 

[Halitim Bachir]

i buildt seprately fftw ,Jdk and mpich2-1.2.1p1 (changed the PRODUCT=mpich2-1.2.1p1 in the build_mpich script), then make a symbolic link to mpich2-1.1 in the thirdparty folder. 

make all went further this time and icps was produced in the /apps/cpseis/platforms/Linux_x86_64_2.17_gfortran_mpich2/bin directory .

Included are the outputs of  make depend  (makedepend file ) and make all (make all file).

 icps was prodcuded but the built stopped , please check make all output file attached in the email.

When running icps testjob1.wrk it keeps searching for cps_mlockfile.dat

[bachir@nexus cpseis]$ icps testjob1.wrk

  

 ===============================================================

 Looping information for file testjob1.wrk

 ===============================================================

  

 loop            1   process numbers            1  thru            4

  

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

NOTE:/apps/cpseis/log/cps_lockfile.dat does not exist-File locking bypassed.

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

bfio.c:2523: Open lockfile /apps/cpseis/log/cps_lockfile.dat failed

 

[Bill Menger]

icps is running, that is good news!  I saw a few errors in the allresults.txt, but it appears that most things have built except for cbyt, va, and csv, cfg, etc.

Try touching a file "/apps/cpseis/log/cps_lockfile.dat and see if that gets rid of the errors from bfio.c:2523.

If it doesn't work, check your config file in the /apps/cpseis/etc directory (grep files for "lockfile") and make sure whatever file you are telling it to look for exists.

Bill

[Halitim Bachir]

i think cfe was built also , please see the attached image file , i used intel compiler  icc version 15.0.3 (gcc version 4.8.5 compatibility) together with ifort 

still have not builf the rest.

the mpich used was   MPICH2 version 1.2.1p1 

the spws build however required #include <jni.h> that i could not find in the cpseis folder.

In file included from /apps/cpseis/spws_home/util/tfio/read_data.c:39:0:

/apps/cpseis/spws_home/include/jsfiles.h:78:17: fatal error: jni.h: No such file or directory

 #include <jni.h>

 

[Bill Menger]

Not sure what's up with missing the jni.h.  I'll look into the jni error.  It might be that the java installation is looking at the wrong version of java from the O/S and not from thirdparty.  It still looks like you are missing the lock file(s).  You should not be getting those errors from bfio.

Bill

[Bill Menger]

I found the jni.h problem.  Go into your /apps/cpseis/thirdparty directory and you will see one java directory:

/apps/cpseis/thirdparty/jdk

Inside it you will find a terrible link "jdk -> /apps/cpseis/thirdparty/jdk"

and a directory "jdk-6u14-linux-x64_x86_64"

and a "platforms" directory

in the platforms directory should be a link from 

your $CPSEIS_ARCH --> /apps/cpseis/thirdparty/jdk/jdk-6u14-linux-x64_x86_64 

It is probably WRONG or not there at all.  It is likely pointing to --> /apps/cpseis/thirdparty/jdk/jdk


This is due to a bug in one of the scripts, and I am working to fix it.  For now, create the link (above in RED)
and go back to /apps/cpseis/platforms/$CPSEIS_ARCH, then type "make" and it should go further.


Sorry for the bug in the build scripts.
Bill

[Halitim Bachir]

Hi Bill,

Exact the make all went further this time , with several warkings, attached is the make depend output together with make all

i used intel compiler 13.3 on Linux nexus 4.14.8-1.el7.elrepo.x86_64, gcc version 4.8.5 20150623 (Red Hat 4.8.5-16) (GCC) ,
jdk-6u45-linux-x64.bin,mpich2-1.2.1p1

----------------- making  programs/cbyt ---------------------
make[2]: Entering directory `/apps/cpseis/spws_home/programs/cbyt/Linux_x86_64_2.17_intel_mpich2'
make[2]: *** No rule to make target `/usr/lib64/libm.a', needed by `cbyt'.  Stop.
make[2]: Leaving directory `/apps/cpseis/spws_home/programs/cbyt/Linux_x86_64_2.17_intel_mpich2'
make[1]: *** [cbyt] Error 2
make[1]: Leaving directory `/apps/cpseis/spws_home/making/Linux_x86_64_2.17_intel_mpich2'
make: *** [cbyt] Error 2

 

[Pedro Valdez]

On Tuesday, February 6, 2018 at 3:49:12 PM UTC+8, Bachir wrote:

Hi Bill,

Exact the make all went further this time , with several warkings, attached is the make depend output together with make all

i used intel compiler 13.3 on Linux nexus 4.14.8-1.el7.elrepo.x86_64, gcc version 4.8.5 20150623 (Red Hat 4.8.5-16) (GCC) ,
jdk-6u45-linux-x64.bin,mpich2-1.2.1p1

----------------- making  programs/cbyt ---------------------
make[2]: Entering directory `/apps/cpseis/spws_home/programs/cbyt/Linux_x86_64_2.17_intel_mpich2'
make[2]: *** No rule to make target `/usr/lib64/libm.a', needed by `cbyt'.  Stop.

Sounds like it can't find libm.a which should be in /usr/lib64
I am not sure if it is always there - maybe depends how you installed Centos (server, desktop, virtrualization, minimal et cetera)
Unfortunately, Centos 7 installer doesn't seem to give you the fine-grained control the older versions had.
Have a look in /usr/lib64 to see if you have libm.a and libm.so. The libm.so should be there. If no libm.a, then try
yum install glibc-static
I presume in the platform makefile in the spws_home/making directory, the MATH_LIBS variable specifies libm.a
You could try changing that to "-lm" which will use the libm.so instead. I recall wrangling that makefile when I have
tried installing on various distros. Sometimes you need the static library, sometimes the shared library works.
 

[Halitim Bachir]

HI Pedro

Thank you for this clarification, i installed the static library glibc-static, then make again , i have the following message,

its searching for /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.so' but the one i have is at 4.8.2.

I have seen on SourceForge Bill is working on that.

I make a symbolic link 4.4.4->4.8.2 and running make again.

Bachir

mpif90  -g -o cbyt cbyt.o -Wl,"-(" wrdc_crou.o wisdom.o string_crou.o swap.o segy_crou.o cbyt_window.o         /usr/lib64/libm.a -lpthread -lc    /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfggui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgxp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfg2d.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgmap.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgqc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libstatgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcube.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libpick.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvfgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvaplots.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libdp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvfgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvf.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvu.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtrslib.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libplot.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvect.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libimage.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libinterp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcubeio.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libhardcopy.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libipc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libwbox.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libnet.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libgeom.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libwproc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libstat.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/liboprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libmodel.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcell.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtfio.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libutlib.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcpsprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtransform.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libinitusage.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcurves.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libsl.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libsp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcolor.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libjseis.a  /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcps.a  /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcgm.a /usr/lib64/libstdc++.so.6 /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.so -L/usr/lib64 -lXm -lXmu -lXp -lXext -lXt -lSM -lICE -lX11 /usr/lib64/libm.a -lpthread -lc -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64 -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server -ljava -ljvm -lverify \
                            /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libfftw.a /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/librfftw.a   -Wl,"-)"
ifort: error #10236: File not found:  '/usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.so'
make[2]: *** [cbyt] Error 1

make[2]: Leaving directory `/apps/cpseis/spws_home/programs/cbyt/Linux_x86_64_2.17_intel_mpich2'
make[1]: *** [cbyt] Error 2
make[1]: Leaving directory `/apps/cpseis/spws_home/making/Linux_x86_64_2.17_intel_mpich2'
make: *** [cbyt] Error 2

[bachir@nexus Linux_x86_64_2.17_intel_mpich2]$

 

--

[Bill Menger]

Halitim,

This make worked better in older less complete versions of linux.. but has always had problems.  I can tell you what I'm doing to address the "makefile says 4.4.4 but I need 4.8.2" problem, but you can solve it with temporary links or whatever you want to get through.  I'm doing this:

in my cpseis_bashrc.sh file (located in ...cpseis/etc and .../cpseis/scripts (for now, keep them synchronized please... working on that too!)

I add this line:

GCCVERSION=$(basename /usr/lib/gcc/x86_64-redhat-linux/*)

then in the ...cpseis/spws_home/making/makefile.$CPSEIS_ARCH i'm changing the "4.4.4" to "$(GCCVERSION)".

I'm still running into a few problems building into CentOS 7.4, but it is coming along.  I got cbyt working today, but still don't have icps working correctly.

Bill

[Halitim Bachir]

making cbyt

I made a symbolic link of 4.4.4 to 4.8.2, when make cybt i end up with the error bellow ,

I am using centos 7 Linux nexus 3.10.0-693.17.1.el7.x86_64.debug #1 and  icc version 15.0.3 (gcc version 4.8.5 compatibility)

cd /apps/cpseis/spws_home/making/Linux_x86_64_2.17_intel_mpich2 && make cbyt 

make[1]: Entering directory `/apps/cpseis/spws_home/making/Linux_x86_64_2.17_intel_mpich2'

----------------- making  programs/cbyt ---------------------

make[2]: Entering directory `/apps/cpseis/spws_home/programs/cbyt/Linux_x86_64_2.17_intel_mpich2'

-------------------------------------------------------

making program  cbyt  in  Linux_x86_64_2.17_intel_mpich2

-------------------------------------------------------

mpif90  -g -o cbyt cbyt.o -Wl,"-(" wrdc_crou.o wisdom.o string_crou.o swap.o segy_crou.o cbyt_window.o         /usr/lib64/libm.a -lpthread -lc    /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfggui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgxp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfg2d.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgmap.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgqc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libstatgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcube.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libpick.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvfgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvaplots.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libdp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvfgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvf.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvu.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtrslib.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libplot.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvect.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libimage.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libinterp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcubeio.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libhardcopy.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libipc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libwbox.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libnet.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libgeom.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libwproc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libstat.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/liboprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libmodel.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcell.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtfio.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libutlib.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcpsprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtransform.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libinitusage.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcurves.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libsl.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libsp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcolor.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libjseis.a  /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcps.a  /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcgm.a /usr/lib64/libstdc++.so.6 /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.so -L/usr/lib64 -lXm -lXmu -lXp -lXext -lXt -lSM -lICE -lX11 /usr/lib64/libm.a -lpthread -lc -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64 -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server -ljava -ljvm -lverify \

                            /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libfftw.a /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/librfftw.a   -Wl,"-)"

cbyt.o: In function `main':

/apps/cpseis/spws_home/programs/cbyt/cbyt.cc:31: multiple definition of `main'

/opt/intel/composer_xe_2015.3.187/compiler/lib/intel64/for_main.o:for_main.c:(.text+0x0): first defined here

/usr/lib64/libm.a(s_floor.o): In function `__floor':

(.text+0x9): undefined reference to `_dl_x86_cpu_features'

/apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcell.a(gtim.o): In function `MAIN__':

/apps/cpseis/spws_home/util/cell/gtim.f:28: undefined reference to `get_idate1_'

/apps/cpseis/spws_home/util/cell/gtim.f:29: undefined reference to `get_itime1_'

/usr/lib64/libm.a(s_atan.o): In function `atan':

(.text+0x25a2): undefined reference to `_dl_x86_cpu_features'

/usr/lib64/libm.a(s_ceil.o): In function `__ceil':

(.text+0x9): undefined reference to `_dl_x86_cpu_features'

/usr/lib64/libm.a(s_sin.o): In function `__cos':

(.text+0x4682): undefined reference to `_dl_x86_cpu_features'

/usr/lib64/libm.a(s_sin.o): In function `__sin':

(.text+0x46b2): undefined reference to `_dl_x86_cpu_features'

/usr/lib64/libm.a(s_tan.o): In function `tan':

(.text+0x5fe2): undefined reference to `_dl_x86_cpu_features'

/usr/lib64/libm.a(e_atan2.o):(.text+0x4b52): more undefined references to `_dl_x86_cpu_features' follow

make[2]: *** [cbyt] Error 1

make[2]: Leaving directory `/apps/cpseis/spws_home/programs/cbyt/Linux_x86_64_2.17_intel_mpich2'

make[1]: *** [cbyt] Error 2

make[1]: Leaving directory `/apps/cpseis/spws_home/making/Linux_x86_64_2.17_intel_mpich2'

make: *** [cbyt] Error 2

 

[Bill Menger]

Go to /apps/cpseis/spws_home/making/makefile.$CPSEIS_ARCH

replace the line: MATH_LIBS = /usr/lib64/libm.a -lpthread -lc

with the line:      MATH_LIBS = -lm -lpthread -lc

and then drop into directory $CPSEIS_ARCH (underneath the "making" directory),

and type

make programs

That should fix the problem of mixing shared libs with static libs from glibc.  The error did not used to cause problems in earlier versions of linux or glibc or gcc.

[Halitim Bachir]

Replaced the MATH_LIBS = /usr/lib64/libm.a -lpthread -lc  with MATH_LIBS = -lm -lpthread -lc

in /apps/cpseis/spws_home/making/makefile.$CPSEIS_ARCH then cd /apps/cpseis/platforms/$CPSEIS_ARCH/

make clean_all,make depend, make all , i have the following error message
mpif90  -g -o cbyt cbyt.o -Wl,"-(" wrdc_crou.o wisdom.o string_crou.o swap.o segy_crou.o cbyt_window.o         -lm -lpthread -lc    /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfggui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgxp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfg2d.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgmap.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgqc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libstatgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcube.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libpick.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvfgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvaplots.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libdp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvfgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvf.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvu.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtrslib.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libplot.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvect.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libimage.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libinterp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcubeio.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libhardcopy.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libipc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libwbox.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libnet.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libgeom.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libwproc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libstat.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/liboprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libmodel.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcell.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtfio.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libutlib.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcpsprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtransform.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libinitusage.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcurves.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libsl.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libsp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcolor.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libjseis.a  /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcps.a  /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcgm.a /usr/lib64/libstdc++.so.6 /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.so -L/usr/lib64 -lXm -lXmu -lXp -lXext -lXt -lSM -lICE -lX11 -lm -lpthread -lc -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64 -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server -ljava -ljvm -lverify \

                            /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libfftw.a /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/librfftw.a   -Wl,"-)"
cbyt.o: In function `main':
/apps/cpseis/spws_home/programs/cbyt/cbyt.cc:31: multiple definition of `main'
/opt/intel/composer_xe_2015.3.187/compiler/lib/intel64/for_main.o:for_main.c:(.text+0x0): first defined here

/apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcell.a(gtim.o): In function `MAIN__':
/apps/cpseis/spws_home/util/cell/gtim.f:28: undefined reference to `get_idate1_'
/apps/cpseis/spws_home/util/cell/gtim.f:29: undefined reference to `get_itime1_'

make[2]: *** [cbyt] Error 1
make[2]: Leaving directory `/apps/cpseis/spws_home/programs/cbyt/Linux_x86_64_2.17_intel_mpich2'
make[1]: *** [cbyt] Error 2
make[1]: Leaving directory `/apps/cpseis/spws_home/making/Linux_x86_64_2.17_intel_mpich2'
make: *** [cbyt] Error 2

 

[Halitim Bachir]

make programs under /apps/cpseis/spws_home/making/Linux_x86_64_2.17_intel_mpich2, only isep was build then stopped building csvtrot
bellow is the outputt of make programs

[bachir@nexus Linux_x86_64_2.17_intel_mpich2]$ pwd
/apps/cpseis/spws_home/making/Linux_x86_64_2.17_intel_mpich2
[bachir@nexus Linux_x86_64_2.17_intel_mpich2]$ ls
%HISTORY_RECORDS  makefile  prefs.xml  prefs.xml.direct.file
[bachir@nexus Linux_x86_64_2.17_intel_mpich2]$ !make
make programs


----------------- making  programs/isep ---------------------
make[1]: Entering directory `/apps/cpseis/spws_home/programs/isep/Linux_x86_64_2.17_intel_mpich2'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/apps/cpseis/spws_home/programs/isep/Linux_x86_64_2.17_intel_mpich2'


----------------- making  programs/csvtrot ---------------------
make[1]: Entering directory `/apps/cpseis/spws_home/programs/csvtrot/Linux_x86_64_2.17_intel_mpich2'

-------------------------------------------------------
making program  csvtrot  in  Linux_x86_64_2.17_intel_mpich2
-------------------------------------------------------
mpif90  -g -o csvtrot csvtrot.o -Wl,"-(" workstation.o         -lm -lpthread -lc    /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfggui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgxp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfg2d.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgmap.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libfgqc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libstatgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcube.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libpick.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvfgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvaplots.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libdp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvfgui.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvf.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvu.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtrslib.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libplot.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libvect.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libimage.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libinterp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcubeio.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libhardcopy.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libipc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libwbox.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libnet.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libgeom.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libwproc.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libstat.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/liboprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libmodel.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcell.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtfio.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libutlib.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcpsprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libtransform.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libinitusage.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcprim.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcurves.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libsl.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libsp.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcolor.a /apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libjseis.a  /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcps.a  /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcgm.a /usr/lib64/libstdc++.so.6 /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.so -L/usr/lib64 -lXm -lXmu -lXp -lXext -lXt -lSM -lICE -lX11 -lm -lpthread -lc -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64 -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server -ljava -ljvm -lverify \
                            /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libfftw.a /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/librfftw.a   -Wl,"-)"
csvtrot.o: In function `main':
/apps/cpseis/spws_home/programs/csvtrot/csvtrot.cc:65: multiple definition of `main'

/opt/intel/composer_xe_2015.3.187/compiler/lib/intel64/for_main.o:for_main.c:(.text+0x0): first defined here
/apps/cpseis/spws_home/spws/lib/Linux_x86_64_2.17_intel_mpich2/libcell.a(gtim.o): In function `MAIN__':
/apps/cpseis/spws_home/util/cell/gtim.f:28: undefined reference to `get_idate1_'
/apps/cpseis/spws_home/util/cell/gtim.f:29: undefined reference to `get_itime1_'

make[1]: *** [csvtrot] Error 1
make[1]: Leaving directory `/apps/cpseis/spws_home/programs/csvtrot/Linux_x86_64_2.17_intel_mpich2'
make: *** [csvtrot] Error 2

 

[Bill Menger]

Look in your make file (located in /apps/cpseis/spws_home/making/makefile.Linux_x86_64_2.17_intel_mpich2) and see if your linking commands have the -nofor_main flag.  without this, the intel compiler will create a main and you have two mains for the program.  

Example from an earlier kernel is attached below (snippet):

  1 #<CPS_v1 type="SCRIPT" pretag="#"/>

  2 ##-------------------------- Linux_x86_64_2.12_intel_intel -------------------------------##

  3 ##-------------------------- Linux_x86_64_2.12_intel_intel -------------------------------##

  4 ##-------------------------- Linux_x86_64_2.12_intel_intel -------------------------------##

  5 

  6 permitted_architectures = Linux_x86_64_2.12_intel_intel

  7 permitted_hosts          = unrestricted

  8 

  9 FC         = mpiifort -c -g

 10 FC_AB90EP  = mpiifort -c -g

 11 FC_O1      = mpiifort -c -g

 12 FC_FLOATIO = mpiifort -c -g

 13 FC_INTERPOLATE  = mpiifort -c -g

 14 FC_KMIG    = mpiifort -c -g

 15 FC_PPIO    = mpiifort -c -g

 16 FC_UNDER   = mpiifort -c -g

 17 FC_LINK    = mpiifort -g -nofor_main

 18 

 19 ### mpicc gave message that -mcmodel=medium not supported in 64 bit mode when using -fPIC

 20 CC         = mpicc -c -g  -Wall -mcmodel=medium -DLINUX -DLINUXI -D_REENTRANT \

 21                                              -D_FILE_OFFSET_BITS=64 \

 22                                              -DIA64 -D_64LINUXI91

 23 CC_LINK    = mpicc

 24 

 25 CXX        = icpc -c -g  -Wall -mcmodel=medium -DLINUX -DLINUXI \

 26                                              -D_FILE_OFFSET_BITS=64 \

 27                                              -DIA64 -D_64LINUXI91

 28 CXX_LINK   = mpiifort  -g -nofor_main

 29 CXX_DEPEND = icpc -MM         -DLINUX -DLINUXI -D_FILE_OFFSET_BITS=64

 30 

 31 PURE_LINK  = @echo "purify not available for this platform."

 32 AR_LINK    = ar -ursv

 33 SO_LINK    = icpc -shared -g

 34 

 35 MODEXT     = .mod

 36 MODFLAG    = -I

 37 FOR_LIBS   = -lstdc++ -liomp5

 38 

[Halitim Bachir]

This is the makefile.$CPSEIS_ARCH located in /apps/cpseis/spws_home/making
as you said i just added the -nofor_main in the FC_LINK and CXX_LINK
and both va and cybt were built , please see the attached screen image of va and cybt
Thanks much for your help and support

#<CPS_v1 type="SCRIPT" pretag="#"/>

##-------------------------- Linux_x86_64_2.17_intel_mpich2 -------------------------------##
##-------------------------- Linux_x86_64_2.17_intel_mpich2 -------------------------------##
##-------------------------- Linux_x86_64_2.17_intel_mpich2 -------------------------------##

permitted_architectures =  Linux_x86_64_2.17_intel_mpich2
permitted_hosts          = nexus

FC         = mpif90 -c -g

FC_AB90EP  = mpif90 -c -g
FC_O1      = mpif90 -c -g
FC_FLOATIO = mpif90 -c -g
FC_INTERPOLATE  = mpif90 -c -g
FC_KMIG    = mpif90 -c -g
FC_PPIO    = mpif90 -c -g
FC_UNDER   = mpif90 -c -g
FC_LINK    = mpif90 -g

### mpicc gave message that -mcmodel=medium not supported in 64 bit mode when using -fPIC

CC         = mpicc -c -g  -Wall -mcmodel=medium -DLINUX -DLINUXI -D_REENTRANT \

                                             -D_FILE_OFFSET_BITS=64 \
                                             -DIA64 -D_64LINUXI91
CC_LINK    = mpicc

CXX        = g++ -c -g  -Wall -mcmodel=medium -DLINUX -DLINUXI \

                                             -D_FILE_OFFSET_BITS=64 \
                                             -DIA64 -D_64LINUXI91
CXX_LINK   = mpif90  -g

CXX_DEPEND = g++ -MM         -DLINUX -DLINUXI -D_FILE_OFFSET_BITS=64

PURE_LINK  = @echo "purify not available for this platform."

AR_LINK    = ar -ursv
SO_LINK    = g++ -shared -g

MODEXT     = .mod
MODFLAG    = -I

FOR_LIBS   = /usr/lib64/libstdc++.so.6 \
             /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.so

GUI_LIBS    = /usr/X11R6/lib64/libXm.a \
              /usr/X11R6/lib64/libXmu.a \
              /usr/X11R6/lib64/libXp.a \
              /usr/X11R6/lib64/libXext.a \
              /usr/X11R6/lib64/libXt.a \
              /usr/X11R6/lib64/libSM.a \
              /usr/X11R6/lib64/libICE.a \
              /usr/X11R6/lib64/libX11.a

GUI_LIBS    = -L/usr/lib64 -lXm -lXmu -lXp -lXext -lXt -lSM -lICE -lX11

#MATH_LIBS  = /usr/lib64/libm.a \
#             /usr/lib64/libpthread.a \
#             /usr/lib64/libc.a
#MATH_LIBS = /usr/lib64/libm.a -lpthread -lc

MATH_LIBS =  -lm -lpthread -lc

JAVA_LIBS = -L$(JAVA_HOME)/jre/lib/amd64 -L$(JAVA_HOME)/jre/lib/amd64/server \
            -ljava -ljvm -lverify

# INCDIRS += /usr/applinux/vendors/openmotif/2.1/include
INCDIRS += $(JAVA_HOME)/include $(JAVA_HOME)/include/linux /usr/include /usr/X11R6/include

 

[Halitim Bachir]

I have the follwing error message when trying to build org.cpseis.util, this is make all outputcfe,
cybt and va were bult with some warning messages. any suggestion  please

Thanks much

BUILDING  liborg_cpseis_util_library.a  in  org.cpseis.util
\rm -rf /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.a
ar rc /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.a /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/CpseisBase.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/CpseisBase_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/GTW.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/GridTransform_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/JniConverter.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/JobRunner.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/PCW.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/PC_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/Pauser.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/cps_startup.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/ftimer.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/ftimer_crou.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/sizetest_crou.o

BUILDING  liborg_cpseis_util_library.so  in  org.cpseis.util
\rm -rf /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.so
gfortran -shared -o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.so /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/CpseisBase.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/CpseisBase_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/GTW.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/GridTransform_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/JniConverter.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/JobRunner.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/PCW.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/PC_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/Pauser.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/cps_startup.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/ftimer.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/ftimer_crou.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/sizetest_crou.o -L/apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lcps -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64 -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server -ljava -ljvm -lverify -L/apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lfftw -lrfftw -L/lib -lmpich -lfmpich   -lstdc++ -lm -lgcc_s -lc -lgcc_s -lutil -lc -lm -lpthread
/usr/bin/ld: cannot find -lmpich
/usr/bin/ld: cannot find -lfmpich
/apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/Pauser.o: In function `Pauser::pause()':
/apps/cpseis/wrappers/src/org/cpseis/util/Pauser.cc:16: warning: the `gets' function is dangerous and should not be used.
collect2: error: ld returned 1 exit status
make[6]: *** [/apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.so] Error 1
make[6]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make[5]: *** [build] Error 2
make[5]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make[4]: *** [util] Error 2
make[4]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis'
make[3]: *** [build] Error 2
make[3]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis'
make[2]: *** [src/org/cpseis] Error 2
make[2]: Leaving directory `/apps/cpseis/wrappers'
make[1]: *** [build] Error 2
make[1]: Leaving directory `/apps/cpseis/wrappers'
make: *** [wrappers] Error 2

 

[Bill Menger]

It looks like your /apps/cpseis/etc/cpseis_bashrc.sh file didn't pick up on your mpi directory correctly.  You could try logging off and back on, and try again, or add this to your LD_LIBRARY_PATH

export LD_LIBRARY_PATH=${MPI_DIR}/lib:$LD_LIBRARY_PATH

Then it should find your mpich libraries.

[Halitim Bachir]

i just  export MPI_DIR=/apps/thirdparty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2 then run
making wrappers
i have the message bellow .
FYI make test run as on normal

cd /apps/cpseis/wrappers && make build
make[1]: Entering directory `/apps/cpseis/wrappers'
make SUBTARGET=build
make[2]: Entering directory `/apps/cpseis/wrappers'
make -C src/org/cpseis build
make[3]: Entering directory `/apps/cpseis/wrappers/src/org/cpseis'
make SUBTARGET=build
make[4]: Entering directory `/apps/cpseis/wrappers/src/org/cpseis'
make -C util build
make[5]: Entering directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make wrappers
make[6]: Entering directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make[6]: Nothing to be done for `wrappers'.

make[6]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'

make java
make[6]: Entering directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make[6]: Nothing to be done for `java'.

make[6]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'

make depend
make[6]: Entering directory `/apps/cpseis/wrappers/src/org/cpseis/util'

CREATING DEPENDENCIES  in  org.cpseis.util
--> input arguments to script make_dependencies...
    CPSEIS_WRAPPERS = /apps/cpseis/wrappers
    JAVA_HOME       = /apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2
    CLASSPATH       = /apps/cpseis/wrappers/classes
    INC_FLAGS       =  -I.  -I/apps/cpseis/wrappers/src/org/cpseis/wrappers  -I/apps/cpseis/wrappers/src/org/cpseis/util  -I/apps/cpseis/src  -I/apps/thirdparty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2/include  -I/apps/thirdpa
rty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/include  -I/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/include/linux
--> getting lists of fortran90 and c and c++ source files...
ls: No match.
--> building fortran90 dependencies...
--> assembling compiler command for building c and c++ dependencies...
--> building c and c++ dependencies...
--> finished
--> your dependencies are now in a local file called makefile.depend

make[6]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'

make lib
make[6]: Entering directory `/apps/cpseis/wrappers/src/org/cpseis/util'

BUILDING  liborg_cpseis_util_library.so  in  org.cpseis.util
\rm -rf /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.so
gfortran -shared -o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.so /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/CpseisBase.o /apps/cpseis/wrappers/platfo
rms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/CpseisBase_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/GTW.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/GridT
ransform_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/JniConverter.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/JobRunner.o /apps/cpseis/wrappers/platforms/Linux
_x86_64_2.17_intel_mpich2/org/cpseis/util/PCW.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/PC_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/Pauser.o /apps/cpseis/
wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/cps_startup.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/ftimer.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cp
seis/util/ftimer_crou.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/sizetest_crou.o -L/apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lcps -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_i

ntel_mpich2/jre/lib/amd64 -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server -ljava -ljvm -lverify -L/apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lfftw -lrfftw -L/apps/thirdp
arty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lmpich -lfmpich    -lstdc++ -lm -lgcc_s -lc -lgcc_s -lutil -lc -lm -lpthread

/apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/Pauser.o: In function `Pauser::pause()':
/apps/cpseis/wrappers/src/org/cpseis/util/Pauser.cc:16: warning: the `gets' function is dangerous and should not be used.

EXAMINING  liborg_cpseis_util_library.so  in  org.cpseis.util
ldd -r /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.so
    linux-vdso.so.1 =>  (0x00007ffddb5b9000)
    libcps.so => /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libcps.so (0x00007efca0fdf000)
    libjava.so => /apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/libjava.so (0x00007efca305f000)
    libjvm.so => /apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server/libjvm.so (0x00007efca03cf000)
    libverify.so => /apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/libverify.so (0x00007efca02c0000)
    libfftw.so.2 => /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libfftw.so.2 (0x00007efca0084000)
    librfftw.so.2 => /apps/thirdparty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib/librfftw.so.2 (0x00007efc9fe52000)
    libmpich.so.1.2 => /apps/thirdparty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libmpich.so.1.2 (0x00007efc9fa35000)
    libfmpich.so.1.2 => /apps/thirdparty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2/lib/libfmpich.so.1.2 (0x00007efc9f812000)
    libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007efc9f50a000)
    libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007efc9f1e8000)
    libm.so.6 => /lib64/libm.so.6 (0x00007efc9eee6000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007efc9ecd0000)
    libc.so.6 => /lib64/libc.so.6 (0x00007efc9e90d000)
    libutil.so.1 => /lib64/libutil.so.1 (0x00007efc9e70a000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00007efc9e4ee000)
    libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007efc9e2b2000)
    librt.so.1 => /lib64/librt.so.1 (0x00007efc9e0aa000)
    libimf.so => /apps/cpseis/intel_x86_64/libimf.so (0x00007efc9dbef000)
    libsvml.so => /apps/cpseis/intel_x86_64/libsvml.so (0x00007efc9cd1c000)
    libmpichf90.so.1.2 => /apps/thirdparty/mpich2-1.2.1p1/lib/libmpichf90.so.1.2 (0x00007efc9cb19000)
    libifport.so.5 => /apps/cpseis/intel_x86_64/libifport.so.5 (0x00007efc9c8ec000)
    libiomp5.so => /apps/cpseis/intel_x86_64/libiomp5.so (0x00007efc9c5af000)
    libintlc.so.5 => /apps/cpseis/intel_x86_64/libintlc.so.5 (0x00007efc9c354000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00007efc9c150000)
    libnsl.so.1 => /lib64/libnsl.so.1 (0x00007efc9bf37000)
    libirng.so => /apps/cpseis/intel_x86_64/libirng.so (0x00007efc9bd30000)
    /lib64/ld-linux-x86-64.so.2 (0x00007efca2f6f000)

make[6]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'

make programs
make[6]: Entering directory `/apps/cpseis/wrappers/src/org/cpseis/util'

BUILDING  liborg_cpseis_util_library.a  in  org.cpseis.util
\rm -rf /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.a
ar rc /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.a /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/CpseisBase.o /apps/cpseis/wrappers/platforms/Linux_x86_6
4_2.17_intel_mpich2/org/cpseis/util/CpseisBase_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/GTW.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/GridTransform_jni.o
/apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/JniConverter.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/JobRunner.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_in
tel_mpich2/org/cpseis/util/PCW.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/PC_jni.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/Pauser.o /apps/cpseis/wrappers/platfo
rms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/cps_startup.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/ftimer.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/ftime
r_crou.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/sizetest_crou.o

LINKING PROGRAM  sizetest  in  org.cpseis.util
gfortran  -o sizetest /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/sizetest.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.a -L/apps/cpseis/platforms/Linu

x_x86_64_2.17_intel_mpich2/lib -lcps -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64 -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server -ljava -ljvm -lverify -L/apps/thirdpa

rty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lfftw -lrfftw -L/apps/thirdparty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lmpich -lfmpich    -lstdc++ -lm -lgcc_s -lc -lgcc_s -lutil -lc -lm -lpthread
/usr/bin/ld: /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/sizetest.o: undefined reference to symbol '__kmpc_end@@VERSION'
/apps/cpseis/intel_x86_64/libiomp5.so: error adding symbols: DSO missing from command line

collect2: error: ld returned 1 exit status

make[6]: *** [sizetest] Error 1

make[6]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make[5]: *** [build] Error 2
make[5]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make[4]: *** [util] Error 2
make[4]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis'
make[3]: *** [build] Error 2
make[3]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis'
make[2]: *** [src/org/cpseis] Error 2
make[2]: Leaving directory `/apps/cpseis/wrappers'
make[1]: *** [build] Error 2
make[1]: Leaving directory `/apps/cpseis/wrappers'
make: *** [wrappers] Error 2

 

[Bill Menger]

Since you have your own intel compiler, remove from the LD_LIBRARY_PATH any reference to /apps/cpseis/intel (perhaps just rename that directory to intel.old) and re-link.  Then your current intel omp libraries will be found and it might link ok.

I put new test jobs into sourceforge yesterday, they will work better than the ones currently in /apps/cpseis/ (testjob1.wrk, testjob2.wrk) which will look for directories that don't exist.

LINKING PROGRAM  sizetest  in  org.cpseis.util
gfortran  -o sizetest /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/sizetest.o /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/lib/liborg_cpseis_util_library.a -L/apps/cpseis/platforms/Linu
x_x86_64_2.17_intel_mpich2/lib -lcps -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64 -L/apps/thirdparty/jdk/platforms/Linux_x86_64_2.17_intel_mpich2/jre/lib/amd64/server -ljava -ljvm -lverify -L/apps/thirdpa
rty/fftw-2.1.5/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lfftw -lrfftw -L/apps/thirdparty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2/lib -lmpich -lfmpich    -lstdc++ -lm -lgcc_s -lc -lgcc_s -lutil -lc -lm -lpthread 
/usr/bin/ld: /apps/cpseis/wrappers/platforms/Linux_x86_64_2.17_intel_mpich2/org/cpseis/util/sizetest.o: undefined reference to symbol '__kmpc_end@@VERSION'

apps/cpseis/intel_x86_64/libiomp5/.so: error adding symbols: DSO missing from command line

collect2: error: ld returned 1 exit status
make[6]: *** [sizetest] Error 1
make[6]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make[5]: *** [build] Error 2
make[5]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis/util'
make[4]: *** [util] Error 2
make[4]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis'
make[3]: *** [build] Error 2
make[3]: Leaving directory `/apps/cpseis/wrappers/src/org/cpseis'
make[2]: *** [src/org/cpseis] Error 2
make[2]: Leaving directory `/apps/cpseis/wrappers'
make[1]: *** [build] Error 2
make[1]: Leaving directory `/apps/cpseis/wrappers'
make: *** [wrappers] Error 2

[Halitim Bachir]

i just renamed the intel folder to intel.old then  export MPI_DIR=/apps/thirdparty/mpich2-1.1/platforms/Linux_x86_64_2.17_intel_mpich2

after make wrappers inside /apps/cpseis/platforms/Linux_x86_64_2.17_intel_mpich2/make wrappers , i have another error message

attached is the output of make wrappers file.

anyone can help on this issue please

thanks much

 

[Bill Menger]

You don't need to make the wrappers.  Those are for people who want to write java or c++ main programs that call cpseis modules.  We just added this to automate building wrappers for other systems that we were porting the modules into.  It looks like a similar error to the last one, it has looked at /apps/cpseis/intel/x86_64.../libomp5.so and should not be looking there.  DSO stands for Dynamic Shared Object.

Go to /apps/cpseis/platforms/$CPSEIS_ARCH and type make;make install;make cfe and you should be up and running.

Bill