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

From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Fri Jan 02 2004 - 12:04:41 CST

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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