Re: Re: Complie NAMD on Suse Linux

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Wed Feb 09 2005 - 17:53:10 CST

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You need fftw lib to compile NAMD, that's why you got:

src/ComputePme.C:8:19: sfftw.h: No such file or directory
src/ComputePme.C:9:20: srfftw.h: No such file or directory

checkout this website for how to compile fftw:
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile

Also change arch/Linux-i686.fftw to setup the correct path to fftw
include and lib dirs.

And yes, NAMD_2.5_Source/arch/Linux-i686-g++.arch is the right file to
remove -static.

Gengbin

Jason Lee wrote:

> Hello, Gengbin:
>
> Thank you very much for your reply. However I didn't find Makefile in
> the NAMD/arch/. Actually this file, Makefile, is in the directory,
> /NAMD_Source_2.5, which doesn't have the -static term. I find the
> -static term in the file /NAMD_2.5_Source/arch/Linux-i686-g++.arch.
> The -static is deleted in the following compilation. The error message
> is as follows.
>
> Could you explain it a little bit? Thank a lot.
>
>
> mkdir inc
> mkdir obj
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/common.o -c src/common.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/common.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/dcdlib.o -c src/dcdlib.C
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/erf.o -c src/erf.C
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/main.ci
> mv main.def.h inc
> mv main.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/WorkDistrib.ci
> mv WorkDistrib.def.h inc
> mv WorkDistrib.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/ReductionMgr.ci
> mv ReductionMgr.def.h inc
> mv ReductionMgr.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/PatchMgr.ci
> mv PatchMgr.def.h inc
> mv PatchMgr.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/ProxyMgr.ci
> mv ProxyMgr.def.h inc
> mv ProxyMgr.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/Node.ci
> mv Node.def.h inc
> mv Node.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/LdbCoordinator.ci
> mv LdbCoordinator.def.h inc
> mv LdbCoordinator.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/NamdCentLB.ci
> mv NamdCentLB.def.h inc
> mv NamdCentLB.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/NamdNborLB.ci
> mv NamdNborLB.def.h inc
> mv NamdNborLB.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/ComputeMgr.ci
> mv ComputeMgr.def.h inc
> mv ComputeMgr.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/ComputePmeMgr.ci
> mv ComputePmeMgr.def.h inc
> mv ComputePmeMgr.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/ComputeExtMgr.ci
> mv ComputeExtMgr.def.h inc
> mv ComputeExtMgr.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/CollectionMgr.ci
> mv CollectionMgr.def.h inc
> mv CollectionMgr.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/CollectionMaster.ci
> mv CollectionMaster.def.h inc
> mv CollectionMaster.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/BroadcastMgr.ci
> mv BroadcastMgr.def.h inc
> mv BroadcastMgr.decl.h inc
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/bin/charmc
> src/Sync.ci
> mv Sync.def.h inc
> mv Sync.decl.h inc
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/main.o -c src/main.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/main.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/mainfunc.o -c src/mainfunc.C
> In file included from /usr/include/g++/backward/strstream:51,
> from src/InfoStream.h:20,
> from src/mainfunc.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/memusage.o -c src/memusage.C
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/strlib.o -c src/strlib.C
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/AlgSeven.o -c src/AlgSeven.C
> In file included from /usr/include/g++/backward/strstream:51,
> from src/InfoStream.h:20,
> from src/AlgSeven.C:8:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/AlgRecBisection.o -c
> src/AlgRecBisection.C
> In file included from /usr/include/g++/backward/strstream:51,
> from src/InfoStream.h:20,
> from src/AlgRecBisection.C:8:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/AlgNbor.o -c src/AlgNbor.C
> In file included from /usr/include/g++/backward/strstream:51,
> from src/InfoStream.h:20,
> from src/AlgNbor.C:8:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/AtomMap.o -c src/AtomMap.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/AtomMap.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/BackEnd.o -c src/BackEnd.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ProcessorPrivate.h:7,
> from src/BackEnd.C:10:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/BroadcastMgr.o -c src/BroadcastMgr.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/BroadcastMgr.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/BroadcastClient.o -c
> src/BroadcastClient.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/BroadcastClient.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/CollectionMaster.o -c
> src/CollectionMaster.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/CollectionMaster.C:10:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/CollectionMgr.o -c
> src/CollectionMgr.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/CollectionMgr.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/Communicate.o -c src/Communicate.C
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/Compute.o -c src/Compute.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Compute.C:14:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeAngles.o -c
> src/ComputeAngles.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/ComputeHomeTuples.h:10,
> from src/ComputeAngles.h:10,
> from src/ComputeAngles.C:14:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeBonds.o -c src/ComputeBonds.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/ComputeBonds.h:11,
> from src/ComputeBonds.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeConsForce.o -c
> src/ComputeConsForce.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/Lattice.h:10,
> from src/SimParameters.h:14,
> from src/ComputeConsForce.C:2:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeConsForceMsgs.o -c
> src/ComputeConsForceMsgs.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ComputeConsForceMsgs.h:10,
> from src/ComputeConsForceMsgs.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeCylindricalBC.o -c
> src/ComputeCylindricalBC.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Compute.h:17,
> from src/ComputePatch.h:14,
> from src/ComputeCylindricalBC.h:10,
> from src/ComputeCylindricalBC.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeDihedrals.o -c
> src/ComputeDihedrals.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/ComputeHomeTuples.h:10,
> from src/ComputeDihedrals.h:10,
> from src/ComputeDihedrals.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeDPME.o -c src/ComputeDPME.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Node.h:16,
> from src/ComputeDPME.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeDPME.C:13:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeDPMEMsgs.o -c
> src/ComputeDPMEMsgs.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ComputeDPMEMsgs.h:10,
> from src/ComputeDPMEMsgs.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeDPMTA.o -c src/ComputeDPMTA.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Node.h:16,
> from src/ComputeDPMTA.C:8:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeDPMTA.C:10:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeEField.o -c
> src/ComputeEField.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Compute.h:17,
> from src/ComputeHomePatch.h:14,
> from src/ComputeEField.h:10,
> from src/ComputeEField.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeExt.o -c src/ComputeExt.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Node.h:16,
> from src/ComputeExt.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeFullDirect.o -c
> src/ComputeFullDirect.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Node.h:16,
> from src/ComputeFullDirect.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeFullDirect.C:12:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeHomePatch.o -c
> src/ComputeHomePatch.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ComputeHomePatch.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeHomePatches.o -c
> src/ComputeHomePatches.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Node.h:16,
> from src/ComputeHomePatches.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeImpropers.o -c
> src/ComputeImpropers.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/ComputeHomeTuples.h:10,
> from src/ComputeImpropers.h:10,
> from src/ComputeImpropers.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeGlobal.o -c
> src/ComputeGlobal.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Node.h:16,
> from src/ComputeGlobal.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeGlobalMsgs.o -c
> src/ComputeGlobalMsgs.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ComputeGlobalMsgs.h:10,
> from src/ComputeGlobalMsgs.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeMap.o -c src/ComputeMap.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ComputeMap.C:10:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeMgr.o -c src/ComputeMgr.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ComputeMgr.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeMgr.C:27:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeNonbondedSelf.o -c
> src/ComputeNonbondedSelf.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Compute.h:17,
> from src/ComputePatch.h:14,
> from src/ComputeNonbondedSelf.h:10,
> from src/ComputeNonbondedSelf.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeNonbondedSelf.h:11,
> from src/ComputeNonbondedSelf.C:7:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeNonbondedPair.o -c
> src/ComputeNonbondedPair.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Compute.h:17,
> from src/ComputePatchPair.h:15,
> from src/ComputeNonbondedPair.h:10,
> from src/ComputeNonbondedPair.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeNonbondedPair.h:11,
> from src/ComputeNonbondedPair.C:7:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeNonbondedUtil.o -c
> src/ComputeNonbondedUtil.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/ComputeNonbondedUtil.h:14,
> from src/ComputeNonbondedUtil.C:17:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeNonbondedUtil.C:17:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeNonbondedStd.o -c
> src/ComputeNonbondedStd.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/ComputeNonbondedUtil.h:14,
> from src/ComputeNonbondedInl.h:18,
> from src/ComputeNonbondedStd.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeNonbondedInl.h:18,
> from src/ComputeNonbondedStd.C:11:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeNonbondedFEP.o -c
> src/ComputeNonbondedFEP.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/ComputeNonbondedUtil.h:14,
> from src/ComputeNonbondedInl.h:18,
> from src/ComputeNonbondedFEP.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeNonbondedInl.h:18,
> from src/ComputeNonbondedFEP.C:11:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputeNonbondedLES.o -c
> src/ComputeNonbondedLES.C
> In file included from /usr/include/g++/backward/new.h:33,
> from src/ResizeArrayRaw.h:19,
> from src/ResizeArray.h:19,
> from src/NamdTypes.h:12,
> from src/ComputeNonbondedUtil.h:14,
> from src/ComputeNonbondedInl.h:18,
> from src/ComputeNonbondedLES.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputeNonbondedInl.h:18,
> from src/ComputeNonbondedLES.C:11:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputePatch.o -c src/ComputePatch.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ComputePatch.C:11:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputePatchPair.o -c
> src/ComputePatchPair.C
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/ComputePatchPair.C:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> -I/home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include
> -DCMK_OPTIMIZE=1 -Isrc -Iinc
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/LINUX/molfile
> -I/home/l0l6571/NAMD_download/Source_code/plugins/LINUX/include
> -I/home/l0l6571/plugins/LINUX -I/home/l0l6571/plugins/LINUX/molfile
> -I/home/l0l6571/plugins/include -DNAMD_PLUGINS -I/usr/include//include
> -I/home/l0l6571/tcl-linux/include -DNAMD_TCL -DUSE_NON_CONST
> -I/usr/include//include -I/home/l0l6571/fftw-linux/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686\" -O3
> -march=pentiumpro -ffast-math -o obj/ComputePme.o -c src/ComputePme.C
> src/ComputePme.C:8:19: sfftw.h: No such file or directory
> src/ComputePme.C:9:20: srfftw.h: No such file or directory
> In file included from /usr/include/g++/backward/new.h:33,
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/init.h:5,
>
>
> from
> /home/l0l6571/NAMD_download/Source_code/NAMD_2.5_Source/charm/net-linux/include/charm++.h:25,
>
>
> from src/Node.h:16,
> from src/ComputePme.C:12:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> 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.
> In file included from src/ComputePme.C:20:
> src/ComputeNonbondedUtil.h: In member function `plint*
> Pairlists::newlist(int)
> ':
> src/ComputeNonbondedUtil.h:34: warning: converting to `int' from `double'
> src/ComputePme.C: At global scope:
> src/ComputePme.C:213: error: syntax error before `,' token
> src/ComputePme.C:214: error: syntax error before `,' token
> src/ComputePme.C:215: error: syntax error before `*' token
> src/ComputePme.C: In constructor `ComputePmeMgr::ComputePmeMgr()':
> src/ComputePme.C:289: error: `work' undeclared (first use this function)
> src/ComputePme.C:289: error: (Each undeclared identifier is reported
> only once for each function it appears in.)
> src/ComputePme.C: In member function `void
> ComputePmeMgr::initialize(CkQdMsg*)
> ':
> src/ComputePme.C:548: error: syntax error before `[' token
> src/ComputePme.C:552: error: `forward_plan_yz' undeclared (first use
> this function)
> src/ComputePme.C:552: error: `FFTW_REAL_TO_COMPLEX' undeclared (first
> use this function)
> src/ComputePme.C:553: error: `FFTW_ESTIMATE' undeclared (first use
> this function)
> src/ComputePme.C:553: error: `FFTW_MEASURE' undeclared (first use this
> function)
> src/ComputePme.C:554: error: `FFTW_IN_PLACE' undeclared (first use
> this function)
> src/ComputePme.C:554: error: `FFTW_USE_WISDOM' undeclared (first use
> this function)
> src/ComputePme.C:554: error: `rfftwnd_create_plan_specific' undeclared
> (first use this function)
> src/ComputePme.C:558: error: `forward_plan_x' undeclared (first use
> this function)
> src/ComputePme.C:560: error: `fftw_complex' undeclared (first use this
> function)
> src/ComputePme.C:560: error: syntax error before `)' token
> src/ComputePme.C:565: error: `backward_plan_x' undeclared (first use
> this function)
> src/ComputePme.C:565: error: `FFTW_COMPLEX_TO_REAL' undeclared (first
> use this function)
> src/ComputePme.C:567: error: syntax error before `)' token
> src/ComputePme.C:572: error: `backward_plan_yz' undeclared (first use
> this function)
> src/ComputePme.C: In member function `void ComputePmeMgr::gridCalc1()':
> src/ComputePme.C:662: error: `rfftwnd_real_to_complex' undeclared
> (first use this function)
> src/ComputePme.C: In member function `void ComputePmeMgr::gridCalc2()':
> src/ComputePme.C:771: error: syntax error before `)' token
> src/ComputePme.C:772: error: `fftw' undeclared (first use this function)
> src/ComputePme.C:783: error: syntax error before `)' token
> src/ComputePme.C: In member function `void ComputePmeMgr::gridCalc3()':
> src/ComputePme.C:889: error: syntax error before `)' token
> src/ComputePme.C:890: error: `rfftwnd_complex_to_real' undeclared
> (first use this function)
> make: *** [obj/ComputePme.o] Error 1
>
> _________________________________________________________________
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