Compiled NAMD on SGI Altix

From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Mon Jan 16 2006 - 18:51:18 CST

Hi, I'm trying to compile NAMD on an SGI Altix (eagle.asc.hpc.mil). I
followed the directions on the wiki. I downloaded the latest charm
(tried both the pre-compiled version and the source). But when I
compile NAMD with

./config tcl fftw Linux-ia64-MPT-icc

I get the following errors during make:

mkdir inc
mkdir obj
icpc -D_IA64 -I/usr/local/gnu/include
-I/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include
-DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include
-I/work1/paramore/NAMD_2.6b1_Source/tcl/linuxia64/include
-I/hafs12/paramore/tcl/include -DNAMD_TCL -DUSE_NON_CONST
-I/work1/paramore/NAMD_2.6b1_Source/fftw/linuxia64/include
-I/hafs12/paramore/include -DNAMD_FFTW -DNAMD_VERSION=\"2.6b1\"
-DNAMD_PLATFORM=\"Linux-ia64-MPT\" -O2 -ftz -IPF_fma -IPF_fltacc
-IPF_flt_eval_method0 -IPF_fp_speculationfast -o obj/common.o -c
src/common.C
/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/pup.h(334):
warning #1476: field uses tail padding of a base class
    int nBytes;
        ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/pup.h(460):
warning #1476: field uses tail padding of a base class
    char line[1000];
         ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/charm++.h(800):
warning #1476: field uses tail padding of a base class
      int _onPE;
          ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/cknodegroupreduction.h(261):
warning #1476: field uses tail padding of a base class
      contributorInfo reductionInfo;//My reduction information
                      ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/ckreduction.h(52):
warning #1476: field uses tail padding of a base class
    int _isReady;
        ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/LBDatabase.h(313):
warning #1476: field uses tail padding of a base class
    int mystep;
        ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/cklocation.h(494):
warning #1476: field uses tail padding of a base class
        CkMagicNumber<CkMigratable> magic; //To detect heap corruption
                                    ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/ckarray.h(338):
warning #1476: field uses tail padding of a base class
        CkArrayIndexMax _idx;//<- our element's array index
                        ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/ckarray.h(436):
warning #1476: field uses tail padding of a base class
    int numElements; /// Initial number of array elements (DEPRICATED)
        ^

/work1/paramore/NAMD_2.6b1_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/include/ckarrayreductionmgr.h(9):
warning #1476: field uses tail padding of a base class
                int size;
                    ^

/usr/include/c++/3.2.3/backward/backward_warning.h(32): warning #1224:
#warning directive: This file includes at least one deprecated or
antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead
of the deprecated header <strstream.h>. To disable this warning use
-Wno-deprecated.
  #warning This file includes at least one deprecated or antiquated
header. \
   ^

/usr/include/c++/3.2.3/limits(1736): error: asm statements not supported
in this environment
        { return __glibcpp_float_signaling_NaN; }
                 ^

/usr/include/c++/3.2.3/limits(1736): error: expected a ")"
        { return __glibcpp_float_signaling_NaN; }
                 ^

/usr/include/c++/3.2.3/limits(1813): error: asm statements not supported
in this environment
        { return __glibcpp_double_signaling_NaN; }
                 ^

/usr/include/c++/3.2.3/limits(1813): error: expected a ")"
        { return __glibcpp_double_signaling_NaN; }
                 ^

/usr/include/c++/3.2.3/limits(1894): error: asm statements not supported
in this environment
        { return __glibcpp_long_double_signaling_NaN; }
                 ^

/usr/include/c++/3.2.3/limits(1894): error: expected a ")"
        { return __glibcpp_long_double_signaling_NaN; }
                 ^

compilation aborted for src/common.C (code 2)
make: *** [obj/common.o] Error 2

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