Re: Compiled NAMD on SGI Altix

From: Margaret Kahn (Margaret.Kahn_at_anu.edu.au)
Date: Mon Jan 16 2006 - 19:13:45 CST

Sterling,

   Depending on which version of the Intel compilers you are using I
have found that I need to include the option

-cxxlib-icc

in Linux-ia64-MPT-icc.arch so that it doesn't try to pick up g++
include files.

   Margaret

On 17/01/2006, at 11:51 AM, Sterling Paramore wrote:

> 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:12 CST