[gmx-users] parallel compilation fails

gleb solomentsev Mon, 21 Jan 2008 10:05:41 -0800

Hi,

I am trying to install a parallel version of Gromacs v3.3.1 and thecompilation fails. I have installed both single and double precisionversions and these work fine, however with the parallel installation Iget the following errors bellow during the make phase. I suppose thatthese are problems with the installed MPI libraries but I am not sure asto the nature of the problem or how to go about solving it. I wouldgreatly appreciate any suggestions and advice.


The cluster is running on x86_64 quad core Intel Xeons.

Thanks in advance,
Gleb

mpicc -O3 -tpp7 -axW -ip -w -o mdrun glaasje.o gctio.o init_sh.oionize.o do_gct.o relax_sh.o repl_ex.o xutils.o md.o mdrun.o genalg.o-L/home/gleb/lib ../mdlib/.libs/libmd_mpi_d.a -L/usr/X11R6/lib64../gmxlib/.libs/libgmx_mpi_d.a -lnsl /home/gleb//lib/libfftw3.a -lm -lXm-lXt -lSM -lICE -lX11

IPO Error: unresolved : _nb_kerne010_x86_64_sse2
       Referenced in libgmx_mpi_d.a(nb_kernel010_x86_64_sse2.o)
IPO Error: unresolved : XShapeQueryExtension
       Referenced in libXm.a(Display.o)
IPO Error: unresolved : XpQueryExtension
       Referenced in libXm.a(ImageCache.o)
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpGetContext
       Referenced in libXm.a(ImageCache.o)
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpGetOneAttribute
       Referenced in libXm.a(ImageCache.o)
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpSetImageResolution
       Referenced in libXm.a(ImageCache.o)
IPO Error: unresolved : XpEndPage
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpEndJob
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpStartPage
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpGetPageDimensions
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpSelectInput
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpGetScreenOfContext
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpGetDocumentData
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : XpGetPdmStartParams
       Referenced in libXm.a(PrintS.o)
IPO Error: unresolved : _XEditResPut8
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResPut32
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResResetStream
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResPutString8
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResGet8
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResGet32
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResGetString8
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResGet16
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResGetWidgetInfo
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResGetSigned16
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResPutWidgetInfo
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : _XEditResPut16
       Referenced in libXm.a(EditresCom.o)
IPO Error: unresolved : XShapeCombineRectangles
       Referenced in libXm.a(DragOverS.o)
IPO Error: unresolved : XShapeCombineMask
       Referenced in libXm.a(DragOverS.o)
make[1]: Leaving directory `/home/gleb/gromacs-3.3.1/src/kernel'

../gmxlib/.libs/libgmx_mpi_d.a(string2.o)(.text+0x2d2): In function`nice_header':: warning: Using 'getpwuid' in statically linked applications requiresat runtime the shared libraries from the glibc version used for linking/usr/X11R6/lib64/libXm.a(Xmos.o)(.text+0x911): In function`XmeGetHomeDirName':: warning: Using 'getpwnam_r' in statically linked applications requiresat runtime the shared libraries from the glibc version used for linking/usr/X11R6/lib64/libXm.a(Xmos.o)(.text+0x95c): In function`XmeGetHomeDirName':: warning: Using 'getpwuid_r' in statically linked applications requiresat runtime the shared libraries from the glibc version used for linking/usr/X11R6/lib64/libICE.a(transport.o)(.text+0x2b3): In function`_IceTransSocketOpen':: warning: Using 'getaddrinfo' in statically linked applicationsrequires at runtime the shared libraries from the glibc version used forlinking/usr/X11R6/lib64/libICE.a(transport.o)(.text+0x388e): In function`_IceTransGetPeerNetworkId':: warning: Using 'gethostbyaddr' in statically linked applicationsrequires at runtime the shared libraries from the glibc version used forlinking/usr/X11R6/lib64/libICE.a(transport.o)(.text+0x1bc7): In function`_IceTransSocketINETConnect':: warning: Using 'gethostbyname' in statically linked applicationsrequires at runtime the shared libraries from the glibc version used forlinking/usr/X11R6/lib64/libICE.a(transport.o)(.text+0x1249): In function`_IceTransSocketINETCreateListener':: warning: Using 'getservbyname' in statically linked applicationsrequires at runtime the shared libraries from the glibc version used forlinking/usr/X11R6/lib64/libXm.a(Display.o)(.text+0x16e): In function`DisplayInitialize':

: undefined reference to `XShapeQueryExtension'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x13a): In function`PrintNotifyHandler':

: undefined reference to `XpEndPage'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x157): In function`PrintNotifyHandler':

: undefined reference to `XpEndJob'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x1e4): In function`PrintNotifyHandler':

: undefined reference to `XpStartPage'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x22f): In function`ResourcesUpdate':

: undefined reference to `XpGetOneAttribute'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x27a): In function`ResourcesUpdate':

: undefined reference to `XpGetPageDimensions'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x38a): In function`SelectXpEvents':

: undefined reference to `XpGetContext'
/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x4a3): In function `Initialize':
: undefined reference to `XpQueryExtension'
/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x4cc): In function `Initialize':
: undefined reference to `XpGetContext'
/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x4e7): In function `Initialize':
: undefined reference to `XpGetScreenOfContext'
/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x67c): In function `Destroy':
: undefined reference to `XpGetContext'
/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x875): In function `FilePipeCB':
: undefined reference to `XpGetContext'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x926): In function`XmPrintToFile':

: undefined reference to `XpGetContext'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0xa82): In function`XmPrintToFile':

: undefined reference to `XpGetDocumentData'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0xc9d): In function`XmPrintPopupPDM':

: undefined reference to `XpGetContext'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0xcfd): In function`XmPrintPopupPDM':

: undefined reference to `XpGetPdmStartParams'

/usr/X11R6/lib64/libXm.a(PrintS.o)(.text+0x3b3): In function`SelectXpEvents':

: undefined reference to `XpSelectInput'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x172): In function`SendCommand':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x17e): In function`SendCommand':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x189): In function`SendCommand':

: undefined reference to `_XEditResPut32'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x213): In function`SendFailure':

: undefined reference to `_XEditResResetStream'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x21e): In function`SendFailure':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x329): In function`GetCommand':

: undefined reference to `_XEditResGet8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x353): In function`GetCommand':

: undefined reference to `_XEditResGet8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x366): In function`GetCommand':

: undefined reference to `_XEditResGet32'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x3c0): In function`GetCommand':

: undefined reference to `_XEditResGetString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x3cc): In function`GetCommand':

: undefined reference to `_XEditResGet16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x3ea): In function`GetCommand':

: undefined reference to `_XEditResGetWidgetInfo'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x43f): In function`GetCommand':

: undefined reference to `_XEditResGet16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x490): In function`GetCommand':

: undefined reference to `_XEditResGetWidgetInfo'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x4a7): In function`GetCommand':

: undefined reference to `_XEditResGetString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x4b7): In function`GetCommand':

: undefined reference to `_XEditResGetString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x503): In function`GetCommand':

: undefined reference to `_XEditResGetWidgetInfo'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x513): In function`GetCommand':

: undefined reference to `_XEditResGetSigned16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x523): In function`GetCommand':

: undefined reference to `_XEditResGetSigned16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x53f): In function`GetCommand':

: undefined reference to `_XEditResResetStream'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x627): In function`GetCommand':

: undefined reference to `_XEditResGet16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x667): In function`GetCommand':

: undefined reference to `_XEditResGet8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x698): In function`GetCommand':

: undefined reference to `_XEditResGet16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x6df): In function`GetCommand':

: undefined reference to `_XEditResGetWidgetInfo'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0xa5f): In function`HandleToolkitErrors':

: undefined reference to `_XEditResPutWidgetInfo'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0xa6e): In function`HandleToolkitErrors':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0xea7): In function`DoSetValues':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0xec5): In function`DoSetValues':

: undefined reference to `_XEditResPutWidgetInfo'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0xed0): In function`DoSetValues':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1021): In function`InsertWidget':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x103d): In function`InsertWidget':

: undefined reference to `_XEditResPut32'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1092): In function`DumpChildren':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x10ad): In function`DumpChildren':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x10c4): In function`DumpChildren':

: undefined reference to `_XEditResPut32'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x11a7): In function`DumpWidgets':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x11c6): In function`DumpWidgets':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1215): In function`DoGetGeometry':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x123e): In function`DoGetGeometry':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1249): In function`DoGetGeometry':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x127c): In function`DoGetGeometry':

: undefined reference to `_XEditResPutWidgetInfo'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x12ca): In function`DoGetGeometry':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x12d4): In function`DoGetGeometry':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x12de): In function`DoGetGeometry':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x13ab): In function`DoGetGeometry':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x13b8): In function`DoGetGeometry':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x13c5): In function`DoGetGeometry':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x13d2): In function`DoGetGeometry':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x13df): In function`DoGetGeometry':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x13ec): In function`DoGetGeometry':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x13f9): In function`DoGetGeometry':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1438): In function`DoGetGeometry':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1442): In function`DoGetGeometry':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x144c): In function`DoGetGeometry':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1462): In function`DoGetGeometry':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x146f): In function`DoGetGeometry':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1782): In function`DoGetResources':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x17a9): In function`DoGetResources':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x17ec): In function`DoGetResources':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1801): In function`DoGetResources':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x181c): In function`DoGetResources':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x182e): In function`DoGetResources':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1840): In function`DoGetResources':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x186e): In function`DoGetResources':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1889): In function`DoGetResources':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x189b): In function`DoGetResources':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x18ad): In function`DoGetResources':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x18f0): In function`DoGetResources':

: undefined reference to `_XEditResPutWidgetInfo'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x191a): In function`DoGetResources':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1925): In function`DoGetResources':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x19a4): In function`DumpValues':

: undefined reference to `_XEditResPut16'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x19de): In function`DumpValues':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x1b7c): In function`DumpValues':

: undefined reference to `_XEditResPutString8'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x202f): In function`_XmEditResCheckMessages':

: undefined reference to `_XEditResResetStream'

/usr/X11R6/lib64/libXm.a(EditresCom.o)(.text+0x2040): In function`_XmEditResCheckMessages':

: undefined reference to `_XEditResPut8'

/usr/X11R6/lib64/libXm.a(DragOverS.o)(.text+0x2e80): In function`_XmDragOverFinish':

: undefined reference to `XShapeCombineRectangles'

/usr/X11R6/lib64/libXm.a(DragOverS.o)(.text+0x351e): In function`DragOverShellPunchHole':

: undefined reference to `XShapeCombineMask'

/usr/X11R6/lib64/libXm.a(DragOverS.o)(.text+0x3574): In function`DragOverShellPunchHole':

: undefined reference to `XShapeCombineRectangles'

/usr/X11R6/lib64/libXm.a(DragOverS.o)(.text+0x35b5): In function`DragOverShellPunchHole':

: undefined reference to `XShapeCombineMask'

/usr/X11R6/lib64/libXm.a(ImageCache.o)(.text+0x1815): In function`_XmPutScaledImage':

: undefined reference to `XpQueryExtension'

/usr/X11R6/lib64/libXm.a(ImageCache.o)(.text+0x182a): In function`_XmPutScaledImage':

: undefined reference to `XpGetContext'

/usr/X11R6/lib64/libXm.a(ImageCache.o)(.text+0x1850): In function`_XmPutScaledImage':

: undefined reference to `XpGetOneAttribute'

/usr/X11R6/lib64/libXm.a(ImageCache.o)(.text+0x1895): In function`_XmPutScaledImage':

: undefined reference to `XpSetImageResolution'

/usr/X11R6/lib64/libXm.a(ImageCache.o)(.text+0x190b): In function`_XmPutScaledImage':

: undefined reference to `XpSetImageResolution'
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/home/gleb/gromacs-3.3.1/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/gleb/gromacs-3.3.1/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/gleb/gromacs-3.3.1/src'
make: *** [all-recursive] Error 1

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[gmx-users] parallel compilation fails

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