Re: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Fri Jan 02 2004 - 12:16:32 CST

Hi,

Please make this change in your charm++ config file at:
charm/src/arch/mpi-linux-ia64/cc-ecc.sh

add -fpic as one command line option to both c and c++ compiler, i.e.
change line:
CMK_CC="ecc $CMK_INCDIR "
to
CMK_CC="ecc -fpic $CMK_INCDIR "

also
CMK_CXX="ecpc $CMK_INCDIR "
to
CMK_CXX="ecpc -fpic $CMK_INCDIR "

please let me know if this fix the compilation and I will commit the
change into cvs.

Gengbin

On Fri, 2 Jan 2004, Jerry Ebalunode wrote:

> Hi Gengbin,
> Sorry it took so long to get back to you. Well here is output during the
> compilation charm++ using intel c+ compiler version 8
> [jebalunode_at_mckinley charm]$ ./build charm++ mpi-linux-ia64 ecc
> Selected Compiler: ecc
> Selected Options:
> Copying src/scripts/Makefile to mpi-linux-ia64-ecc/tmp
> Soft-linking over bin
> Soft-linking over lib
> Soft-linking over lib_so
> Soft-linking over include
> Soft-linking over tmp
> Generating mpi-linux-ia64-ecc/tmp/conv-mach-pre.sh
> Performing 'make charm++ OPTS=' in mpi-linux-ia64-ecc/tmp
> make headerlinks
> make[1]: Entering directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> ../bin/charmc -native -language c++ -cp ../bin/ -o charmxi xi-main.o
> xi-symbol.o xi-grammar.tab.o xi-scan.o xi-util.o sdag-globals.o
> CSdagConstruct.o CEntry.o
> ../bin/charmc -intrinsic -build-shared ckcallback.ci
> ../bin/charmc -intrinsic -build-shared ckmarshall.ci
> ../bin/charmc -intrinsic -build-shared ckarray.ci
> ../bin/charmc -intrinsic -build-shared cklocation.ci
> ../bin/charmc -intrinsic -build-shared ckreduction.ci
> ../bin/charmc -intrinsic -build-shared ckarrayreductionmgr.ci
> ../bin/charmc -intrinsic -build-shared tempo.ci
> ../bin/charmc -intrinsic -build-shared waitqd.ci
> ../bin/charmc -intrinsic -build-shared ckfutures.ci
> ../bin/charmc -intrinsic -build-shared ckcheckpoint.ci
> ../bin/charmc -intrinsic -build-shared LBDatabase.ci
> ../bin/charmc -intrinsic -build-shared CentralLB.ci
> ../bin/charmc -intrinsic -build-shared ComboCentLB.ci
> ../bin/charmc -intrinsic -build-shared NullLB.ci
> ../bin/charmc -intrinsic -build-shared RandCentLB.ci
> ../bin/charmc -intrinsic -build-shared RecBisectBfLB.ci
> ../bin/charmc -intrinsic -build-shared BaseLB.ci
> ../bin/charmc -intrinsic -build-shared MetisLB.ci
> ../bin/charmc -intrinsic -build-shared DummyLB.ci
> ../bin/charmc -intrinsic -build-shared RefineLB.ci
> ../bin/charmc -intrinsic -build-shared RefineCommLB.ci
> ../bin/charmc -intrinsic -build-shared OrbLB.ci
> ../bin/charmc -intrinsic -build-shared GreedyLB.ci
> ../bin/charmc -intrinsic -build-shared NborBaseLB.ci
> ../bin/charmc -intrinsic -build-shared NeighborLB.ci
> ../bin/charmc -intrinsic -build-shared NeighborCommLB.ci
> ../bin/charmc -intrinsic -build-shared WSLB.ci
> ../bin/charmc -intrinsic -build-shared GreedyRefLB.ci
> ../bin/charmc -intrinsic -build-shared RandRefLB.ci
> ../bin/charmc -intrinsic -build-shared GreedyCommLB.ci
> ../bin/charmc -intrinsic -build-shared Comm1LB.ci
> ../bin/charmc -intrinsic -build-shared EveryLB.ci
> ../bin/charmc -intrinsic -build-shared charisma.ci
> ../bin/charmc -intrinsic -build-shared trace-summary.ci
> ../bin/charmc -intrinsic -build-shared BlueGene.ci
> Soft-linking headers...
> make[1]: [headerlinks] Error 1 (ignored)
> touch headerlinks
> make[1]: Leaving directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> touch basics
> make charm-target
> make[1]: Entering directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> make headerlinks
> make[2]: Entering directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> make[2]: `headerlinks' is up to date.
> make[2]: Leaving directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> touch basics
> make QuickThreads/libqt.a
> make[2]: Entering directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> make[2]: `QuickThreads/libqt.a' is up to date.
> make[2]: Leaving directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> make converse-target
> make[2]: Entering directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> ../bin/charmc -build-shared -c -I. convcore.c
> convcore.c(2004): warning #266: function declared implicitly
> CmiTimerInit();
> ^
>
> ../bin/charmc -build-shared -c -I. conv-conds.c
> ../bin/charmc -build-shared -c -I. queueing.c
> ../bin/charmc -build-shared -c -I. msgmgr.c
> ../bin/charmc -build-shared -c -I. cpm.c
> ../bin/charmc -build-shared -c -I. cpthreads.c
> ../bin/charmc -build-shared -c -I. futures.c
> ../bin/charmc -build-shared -c -I. cldb.c
> ../bin/charmc -build-shared -c -I. topology.C
> ../bin/charmc -build-shared -c -I. random.c
> ../bin/charmc -build-shared -c -I. debug-conv.c
> ../bin/charmc -build-shared -c -I. generate.c
> ../bin/charmc -build-shared -c -I. edgelist.c
> edgelist.c(58): warning #1193: standard requires that parameter "x" be given a
> type by a subsequent declaration ("int" assumed)
> int edgeExists(x,y)
> ^
>
> edgelist.c(58): warning #1193: standard requires that parameter "y" be given a
> type by a subsequent declaration ("int" assumed)
> int edgeExists(x,y)
> ^
>
> ../bin/charmc -build-shared -c -I. conv-ccs.c
> ccs-server.c(311): warning #266: function declared implicitly
> if (isxdigit(key[0]) && isxdigit(key[1]))
> ^
>
> ccs-server.c(353): warning #167: argument of type "unsigned int *far" is
> incompatible with parameter of type "int *far"
> ccs_server_fd=skt_server(&port);
> ^
>
> ccs-server.c(416): warning #167: argument of type "unsigned int *far" is
> incompatible with parameter of type "int *far"
> fd=skt_accept(ccs_server_fd,&ip,&port);
> ^
>
> ../bin/charmc -build-shared -c -I. ccs-builtins.C
> ../bin/charmc -build-shared -c -I. traceCore.C
> traceCoreAPI.h(8): warning #380: linkage specification is incompatible with
> previous "Cpv__traceCoreOn_" (declared at line 20 of "traceCore.h")
> CpvExtern(int,_traceCoreOn);
> ^
>
> ../bin/charmc -build-shared -c -I. traceCoreCommon.C
> traceCoreAPI.h(8): warning #380: linkage specification is incompatible with
> previous "Cpv__traceCoreOn_" (declared at line 20 of "traceCore.h")
> CpvExtern(int,_traceCoreOn);
> ^
>
> ../bin/charmc -build-shared -c -I. converseProjections.C
> ../bin/charmc -build-shared -c -I. machineProjections.C
> ../bin/charmc -build-shared -c -I. quiescence.c
> ../bin/charmc -build-shared -c -I. isomalloc.c
> ../bin/charmc -build-shared -c -I. global-nop.c
> ../bin/charmc -build-shared -o ../lib/libconv-core.a convcore.o conv-conds.o
> queueing.o msgmgr.o cpm.o cpthreads.o futures.o cldb.o topology.o random.o
> debug-conv.o generate.o edgelist.o conv-ccs.o ccs-builtins.o traceCore.o
> traceCoreCommon.o converseProjections.o machineProjections.o quiescence.o
> isomalloc.o global-nop.o
> Warning: creating ../lib_so/libconv-core.so
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> keys_inactive
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> keys_inactive
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_current_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_current_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_current_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_current_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_current_
> /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol
> Csv_CtvOffsCpthread_errcode_
> Fatal Error by charmc in
> directory /tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp
> Command icc -L/opt/scali/lib -lmpi -o ../lib_so/libconv-core.so -shared
> -L/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/lib_so
> convcore.o conv-conds.o queueing.o msgmgr.o cpm.o cpthreads.o futures.o
> cldb.o topology.o random.o debug-conv.o generate.o edgelist.o conv-ccs.o
> ccs-builtins.o traceCore.o traceCoreCommon.o converseProjections.o
> machineProjections.o quiescence.o isomalloc.o global-nop.o returned error
> code 1
> charmc exiting...
> make[2]: *** [../lib/libconv-core.a] Error 1
> make[2]: Leaving directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> make[1]: *** [converse] Error 2
> make[1]: Leaving directory
> `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp'
> make: *** [charm++] Error 2
>
> On Wednesday 31 December 2003 01:25 pm, Gengbin Zheng wrote:
> > I don't have access to Intel C++ compilers v8.0 on IA64. Could you copy me
> > the compile error messages?
> >
> > Gengbin
> >
> > On Wed, 31 Dec 2003, Jerry Ebalunode wrote:
> > > Hi,
> > > I would like to know if Charm++ and then NAMD can be built using the new
> > > intel C++ compiler version 8.0 on an IA64 arch. I already tried this on
> > > the charm++ source code that was provided along with the namd ver2.5.,
> > > with no succes in compling charm++ for mpi-linux-ia64.
> > >
> > > On Wednesday 31 December 2003 11:59 am, Gengbin Zheng wrote:
> > > > Oops, forgot to mention, you need to recompile Linux version of NAMD
> > > > from scratch also. The pre-compiled version is not compatiable with the
> > > > latest CVS version due to my recent changes in structure layout. Also,
> > > > the pre-compiled version is built with Intel C++ compiler which I have
> > > > not tested the compatibility with Win32 VC++ yet. So I would suggest
> > > > going with gcc on Linux before I tested it with Intel C++.
> > > >
> > > > Since I don't know which verison of Linux you are running, I don't know
> > > > how to make pre-compiled binary for you. But compiling for Linux is
> > > > fairely easy, check out:
> > > > http://www.ks.uiuc.edu/Research/namd/development.html
> > > > Please download both Charm++ and NAMD source from the two different CVS
> > > > servers.
> > > >
> > > > I myself rarely use tcl and plugins features (being a mostly Charm++
> > > > developer). Based on my limited knowledge, tcl is used to enable
> > > > scripting features (so you can write tcl scripts in config file), and
> > > > plugins tools are from VMD's Plugins to enable trajectory analysis. The
> > > > NAMD user manual should have more detailed information.
> > > >
> > > > Gengbin
> > > >
> > > > On Wed, 31 Dec 2003, Gadi Oron wrote:
> > > > > On Wed, 2003-12-31 at 02:05, Gengbin Zheng wrote:
> > > > > > Hi,
> > > > > >
> > > > > > Please find the NAMD binary compiled with Windows VC++ 6.0 at:
> > > > > > http://www.ks.uiuc.edu/~gzheng/NAMD_Win32-i686.zip
> > > > >
> > > > > Thank you, but still no luck...
> > > > > I manage to start NAMD alone on a Win2K node and on Linux node,
> > > > > so probably my nodelist is Ok. But together I get either:
> > > > >
> > > > > Info: SUMMARY OF PARAMETERS:
> > > > > Info: 180 BONDS
> > > > > Info: 442 ANGLES
> > > > > Info: 534 DIHEDRAL
> > > > > Info: 50 IMPROPER
> > > > > Info: 91 VDW
> > > > > Info: 0 VDW_PAIRS
> > > > > Charmrun: error on request socket--
> > > > > Error on socket recv!
> > > > >
> > > > > when the Linux box is first in the nodelist and:
> > > > >
> > > > > Charmrun> node programs all connected
> > > > > ------------- Processor 1 Exiting: Caught Signal ------------
> > > > > Signal: segmentation violation
> > > > > Suggestion: Try running with '++debug', or linking with '-memory
> > > > > paranoid'.
> > > > > Fatal error on PE 1> segmentation violation
> > > > >
> > > > > when the order is inverted.
> > > > >
> > > > > I am using charmd compiled from the last source and NAMD 2.5 from
> > > > > the pre-compiled binaries for linux and your Windows executables.
> > > > >
> > > > > Any idea?
> > > > >
> > > > > Best regards.
> > > > >
> > > > > P.S. It is not really explained what "plugins" and "tcl" libraries
> > > > > are needed for... Could you give me a hint on that?
> > > > > --
> > > > > ================= Gadi ORON, PhD -o- Proteologics
> > > > > ====================== ========== gadi/at/proteologics.com ==========
> > > > > +972 8 9475666 ========== The questions remain the same. The answers
> > > > > are eternally variable.
> > >
> > > --
> > > Cheers,
> > >
> > > Jerry Ebalunode
> > > Graduate Research Assistant
> > > RM 402F Houston Science Center
> > > Phone: 713-743-8367
> > > Dept. of Biology and Biochemistry
> > > University of Houston.
> > > 4800 Calhoun Road
> > > Houston, TX 77204
>
> --
> Cheers,
>
> Jerry Ebalunode
> Graduate Research Assistant
> RM 402F Houston Science Center
> Phone: 713-743-8367
> Dept. of Biology and Biochemistry
> University of Houston.
> 4800 Calhoun Road
> Houston, TX 77204
>

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