Re: namd on Altix

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Tue Mar 08 2005 - 18:43:47 CST

yes, you need to recompile Charm in that case.

cd ~/namd/charm-mpi-linux-ia64-ifort-mpt-icc/
remove the directory mpi-linux-ia64-ifort-mpt-icc

and run:

./build charm++ mpi-linux-ia64 ifort mpt icc -O -DCMK_OPTIMIZE

Gengbin

Michel Espinoza-Fonseca wrote:

>Thank you very much. Seem to be that now is working. I have another
>question. The system is asking me for the library libstdc++.so.5, but I
>have the version libstdc++.so.3. Do you think I have to compile charm++
>with the libraries we have? I guess it'll solve the problem.
>
>What I get is:
>
>/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-i
>a64-ifort-mpt-icc/bin/charmc src/main.ci
>/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-i
>a64-ifort-mpt-icc/bin/charmxi: error while loading shared libraries:
>libstdc++.so.5: cannot open shared object file: No such file or
>directory
>Fatal Error by charmc in directory
>/home/bscl2/espinoza/namd/NAMD_2.5_Source/Linux-ia64-MPT-icc
> Command
>/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-i
>a64-ifort-mpt-icc/bin/charmxi src/main.ci returned error code 127
>charmc exiting...
>
>Michel
>
>-----Original Message-----
>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu]
>Sent: Tuesday, March 08, 2005 5:21 PM
>To: Michel Espinoza-Fonseca
>Cc: namd-l_at_ks.uiuc.edu
>Subject: Re: namd-l: namd on Altix
>
>
>ok, do a
>ls
>~/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-icc/i
>nclude
>
>see if the directory is there.
>
>If this is not the problem, change your CHARMBASE in Make.charm to:
>$(HOME/namd/charm-mpi-linux-ia64-ifort-mpt-icc
>avoid '~' in Makefile.
>
>Gengbin
>
>
>Michel Espinoza-Fonseca wrote:
>
>
>
>>This is the error line I got:
>>
>>mkdir inc
>>mkdir obj
>>ecpc -D_IA64 -I/usr/local/gnu/include -DSOCKLEN_T=socklen_t
>>-I~/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-ic
>>
>>
>c
>
>
>>/include -DCMK_OPTIMIZE=1 -Isrc -Iinc -I~/namd/LINUXIA64/LINUXIA64
>>-I~/namd/LINUXIA64/LINUXIA64/molfile -I~/namd/LINUXIA64/include
>>-I/home/bscl2/espinoza/plugins/LINUXIA64
>>-I/home/bscl2/espinoza/plugins/LINUXIA64/molfile
>>-I/home/bscl2/espinoza/plugins/include -DNAMD_PLUGINS
>>-I~/namd/linuxia64/include -I/home/bscl2/espinoza/tcl/include
>>
>>
>-DNAMD_TCL
>
>
>>-DUSE_NON_CONST -I~/namd/linuxia64/include
>>-I/home/bscl2/espinoza/fftw-linux/include -DNAMD_FFTW
>>-DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-ia64\" -O2 -ftz
>>
>>
>-IPF_fma
>
>
>>-IPF_fltacc -IPF_flt_eval_method0 -IPF_fp_speculationfast -o
>>obj/common.o -c src/common.C
>>ecpc: warning: The Intel C/C++ driver is now named icpc. You can
>>suppress this message with '-quiet'
>>src/common.C(11): catastrophic error: could not open source file
>>"charm++.h"
>> #include "charm++.h"
>> ^
>>
>>compilation aborted for src/common.C (code 4)
>>make: *** [obj/common.o] Error 4
>>
>>Michel
>>
>>-----Original Message-----
>>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu]
>>Sent: Tuesday, March 08, 2005 5:10 PM
>>To: Michel Espinoza-Fonseca
>>Cc: namd-l_at_ks.uiuc.edu
>>Subject: Re: namd-l: namd on Altix
>>
>>
>>I meant the actually ecpc command line that give you the error
>>"charm++.h not found"
>>
>>Gengbn
>>
>>Michel Espinoza-Fonseca wrote:
>>
>>
>>
>>
>>
>>>Both CHARMBASE and CHARMARCH are correct. Here is the arch file
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>>>>>>include .rootdir/arch/Linux-ia64-ecc.arch
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>> CHARMARCH=mpi-linux-ia64-ifort-mpt-icc <<<<<<
>>>
>>>And then in Linux-ia64-ecc.arch I have:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>>>>>NAMD_ARCH = Linux-ia64
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>CHARMARCH = mpi-linux-ia64-ifort-mpt-icc
>>>
>>>FLOATOPTS = -ftz -IPF_fma -IPF_fltacc -IPF_flt_eval_method0
>>>-IPF_fp_speculationfast
>>>
>>>CXX = ecpc -D_IA64 -I/usr/local/gnu/include -DSOCKLEN_T=socklen_t
>>>CXXOPTS = -O2 $(FLOATOPTS)
>>>CXXNOALIASOPTS = -O2 -fno-alias $(FLOATOPTS) -opt_report \
>>> -opt_report_levelmin -opt_report_routinecalc_
>>>
>>>CC = icc
>>>COPTS = -O2 $(FLOATOPTS) <<<<
>>>
>>>About this command invoking ecpc, it is found in this second file
>>>Linux-ia64-ecc.arch.
>>>
>>>For that reason I don't know what's going on here.
>>>Thanks,
>>>Michel
>>>
>>>-----Original Message-----
>>>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu]
>>>Sent: Tuesday, March 08, 2005 5:00 PM
>>>To: Michel Espinoza-Fonseca
>>>Cc: namd-l_at_ks.uiuc.edu
>>>Subject: Re: namd-l: namd on Altix
>>>
>>>
>>>You need both CHARMBASE and CHARMARCH correct.
>>>
>>>What is the command that invokes ecpc?
>>>
>>>Gengbin
>>>
>>>Michel Espinoza-Fonseca wrote:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>>Sorry, but it is exactly what I did. I changed the CHARMBASE to
>>>>~/namd/charm-mpi-linux-ia64-ifort-mpt-icc (this is the actual root
>>>>
>>>>
>dir
>
>
>>>>for charm), but still it didn't work. I was trying several times
>>>>
>>>>
>>>>
>>>>
>>before
>>
>>
>>
>>
>>>>writing again, but I don't know...
>>>>
>>>>Michel
>>>>
>>>>-----Original Message-----
>>>>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu]
>>>>Sent: Tuesday, March 08, 2005 4:54 PM
>>>>To: Michel Espinoza-Fonseca
>>>>Cc: namd-l_at_ks.uiuc.edu
>>>>Subject: Re: namd-l: namd on Altix
>>>>
>>>>
>>>>I think I have explained how it works:
>>>>
>>>>In Make.charm, you give CHARMBASE
>>>>In the config_version.arch (where config_version is the version you
>>>>config NAMD in the ./config command line), you defines CHARMARCH
>>>>
>>>>And the include search path is now:
>>>>
>>>>
>$(CHARMBASE)/$(CHARMARCH)/include
>
>
>>>>And you need to make it right to your charm installation path.
>>>>
>>>>Just looks for the actual command below in -I flag to see if you have
>>>>
>>>>
>
>
>
>>>>made that right.
>>>>
>>>>ecpc -D_IA64 -I/usr/local/gnu/include -DSOCKLEN_T=socklen_t
>>>>-I~/namd/NAMD_2.5_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux
>>>>
>>>>
>-
>
>
>>>>
>>>>
>>>>
>>>>
>>i
>>
>>
>>
>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>a
>>>
>>>
>>>
>>>
>>>
>>>
>>>>64-ifort-mpt-icc/include/mpi-linux-ia64-gm/include
>>>>
>>>>
>>>>Gengbin
>>>>
>>>>Michel Espinoza-Fonseca wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>Hi again,
>>>>>I did exactly what you told me, but I still get the same error
>>>>>(charm++.h can't be read). I really don't know what's happening.
>>>>>I hope you can help me.
>>>>>Thank you,
>>>>>Michel
>>>>>
>>>>>-----Original Message-----
>>>>>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu]
>>>>>Sent: Monday, March 07, 2005 6:59 PM
>>>>>To: Michel Espinoza-Fonseca
>>>>>Cc: namd-l_at_ks.uiuc.edu
>>>>>Subject: Re: namd-l: namd on Altix
>>>>>
>>>>>
>>>>>see what is in your command line about the -I option:
>>>>>
>>>>>ecpc -D_IA64 -I/usr/local/gnu/include -DSOCKLEN_T=socklen_t
>>>>>-I~/namd/NAMD_2.5_Source/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linu
>>>>>
>>>>>
>x
>
>
>>>>>
>>>>>
>>>>>
>>>>>
>>-
>>
>>
>>
>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>i
>>>
>>>
>>>
>>>
>>>
>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>a
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>64-ifort-mpt-icc/include/mpi-linux-ia64-gm/include
>>>>>
>>>>>Of course I don't think you have that include directory.
>>>>>
>>>>>first, you must have put
>>>>>
>>>>>mpi-linux-ia64-ifort-mpt-icc/include in Make.charm, which like I
>>>>>
>>>>>
>>>>>
>>>>>
>>said,
>>
>>
>>
>>
>>>>>you can't do that since the config arch file will append
>>>>>$(CHARMARCH)/include automatically.
>>>>>Your Make.charm should have just the charm base
>>>>>~/namd/NAMD_2.5_Source/charm-mpi-linux-ia64-ifort-mpt-icc
>>>>>
>>>>>and second, if you choose to config namd like:
>>>>>config namd2/arch/Linux-ia64-MPI-GM-ecc
>>>>>
>>>>>then you are saying you have myrinet on Altix??
>>>>>
>>>>>If that's the case (I doubt), it then looks for
>>>>>arch/Linux-ia64-MPI-GM-ecc.arch file, and
>>>>>
>>>>>
>CHARMARCH=mpi-linux-ia64-gm
>
>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>in
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>it.
>>>>>That is namd assumes you have compiled "mpi-linux-ia64-gm" version
>>>>>
>>>>>
>of
>
>
>>>>>
>>>>>
>>>>>
>>>>>
>>
>>
>>
>>
>>>>>Charm, and it appends mpi-linux-ia64-gm/include in -I option above.
>>>>>
>>>>>
>
>
>
>>>>>However, you certainly don't have "mpi-linux-ia64-gm".
>>>>>
>>>>>Like I said, we config NAMD on altix like:
>>>>>
>>>>>./config fftw ... Linux-ia64-MPT-icc
>>>>>
>>>>>And modify Linux-ia64-MPT-icc.arch to have
>>>>>CHARMARCH=mpi-linux-ia64-ifort-mpt-icc like I mentioned before.
>>>>>
>>>>>Gengbin
>>>>>
>>>>>
>>>>>Michel Espinoza-Fonseca wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>This is what I have in the file /../arch/Linux-ia64-MPT-icc.arch
>>>>>>
>>>>>>include .rootdir/arch/Linux-ia64-ecc.arch
>>>>>>CHARMARCH = mpi-linux-ia64-gm
>>>>>>
>>>>>>Then going the file Linux-ia64-ecc.arch, I have this:
>>>>>>
>>>>>>NAMD_ARCH = Linux-ia64
>>>>>>CHARMARCH = net-linux-ia64-ecc
>>>>>>
>>>>>>FLOATOPTS = -ftz -IPF_fma -IPF_fltacc -IPF_flt_eval_method0
>>>>>>-IPF_fp_speculationfast
>>>>>>
>>>>>>CXX = ecpc -D_IA64 -I/usr/local/gnu/include -DSOCKLEN_T=socklen_t
>>>>>>CXXOPTS = -O2 $(FLOATOPTS)
>>>>>>CXXNOALIASOPTS = -O2 -fno-alias $(FLOATOPTS) -opt_report \
>>>>>> -opt_report_levelmin -opt_report_routinecalc_
>>>>>>
>>>>>>CC = ecc
>>>>>>COPTS = -O2 $(FLOATOPTS)
>>>>>>
>>>>>>At the end I downloaded the compiled version of charm++
>>>>>>(/mpi-linux-ia64-ifort-mpt-icc) and I stored all files in a dir.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>Thus,
>>>
>>>
>>>
>>>
>>>
>>>
>>>>>>when I did:
>>>>>>
>>>>>>$config tcl fftw plugins Linux-ia64-MPI-GM-ecc
>>>>>>
>>>>>>And then 'make' on the dir 'Linux-ia64-MPI-GM-ecc', I got this:
>>>>>>
>>>>>>mkdir inc
>>>>>>mkdir obj
>>>>>>ecpc -D_IA64 -I/usr/local/gnu/include -DSOCKLEN_T=socklen_t
>>>>>>-I~/namd/NAMD_2.5_So
>>>>>>urce/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-ia64-ifort-mpt-ic
>>>>>>
>>>>>>
>c
>
>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>/
>>
>>
>>
>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>i
>>>
>>>
>>>
>>>
>>>
>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>n
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>c
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>lude/mpi
>>>>>>-linux-ia64-gm/include -DCMK_OPTIMIZE=1 -Isrc -Iinc
>>>>>>-I~/namd/LINUXIA64/LINUXIA
>>>>>>64 -I~/namd/LINUXIA64/LINUXIA64/molfile -I~/namd/LINUXIA64/include
>>>>>>-I/home/bscl2
>>>>>>/espinoza/plugins/LINUXIA64
>>>>>>-I/home/bscl2/espinoza/plugins/LINUXIA64/molfile -I/
>>>>>>home/bscl2/espinoza/plugins/include -DNAMD_PLUGINS
>>>>>>-I~/namd/linuxia64/include -I
>>>>>>/home/bscl2/espinoza/tcl/include -DNAMD_TCL -DUSE_NON_CONST
>>>>>>-I~/namd/linuxia64/i
>>>>>>nclude -I/home/bscl2/espinoza/fftw-linux/include -DNAMD_FFTW
>>>>>>-DNAMD_VERSION=\"2
>>>>>>.5\" -DNAMD_PLATFORM=\"Linux-ia64-MPI-GM\" -O2 -ftz -IPF_fma
>>>>>>-IPF_fltacc -IPF_f
>>>>>>lt_eval_method0 -IPF_fp_speculationfast -o obj/common.o -c
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>src/common.C
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>ecpc: warning: The Intel C/C++ driver is now named icpc. You can
>>>>>>suppress this
>>>>>>message with '-quiet'
>>>>>>src/common.C(11): catastrophic error: could not open source file
>>>>>>"charm++.h"
>>>>>>#include "charm++.h"
>>>>>> ^
>>>>>>compilation aborted for src/common.C (code 4)
>>>>>>make: *** [obj/common.o] Error 4
>>>>>>
>>>>>>I got this error even though I changed many times the location of
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>the
>>
>>
>>
>>
>>>>>>charm parent dir. What I originally had in the file Make.charm was:
>>>>>>
>>>>>># Set CHARMBASE to the top level charm directory.
>>>>>>
>>>>>>CHARMBASE =
>>>>>>/home/bscl2/espinoza/namd/NAMD_2.5_Source/charm-mpi-linux-ia64-ifor
>>>>>>
>>>>>>
>t
>
>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>-
>>
>>
>>
>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>m
>>>
>>>
>>>
>>>
>>>
>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>p
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>t
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>-icc/mpi-linux-ia64-ifort-mpt-icc
>>>>>>#CHARMBASE = C:/cygwin$(HOME)/charm
>>>>>>
>>>>>>So I hope this information will be useful for getting helped.
>>>>>>Thank you.
>>>>>>
>>>>>>Cheers,
>>>>>>Michel
>>>>>>
>>>>>>-----Original Message-----
>>>>>>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu]
>>>>>>Sent: Monday, March 07, 2005 6:28 PM
>>>>>>To: Gengbin Zheng
>>>>>>Cc: Michel Espinoza-Fonseca; namd-l_at_ks.uiuc.edu
>>>>>>Subject: Re: namd-l: namd on Altix
>>>>>>
>>>>>>
>>>>>>
>>>>>>Show us the what's in file namd2/arch/Linux-ia64-MPT-icc.arch
>>>>>>And your build command to compile charm and namd.
>>>>>>
>>>>>>Gengbin Zheng wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Like I said, you need to modify CHARMARCH in
>>>>>>>namd2/arch/Linux-ia64-MPT-icc.arch
>>>>>>>assuming you configured namd using:
>>>>>>>
>>>>>>>./config .... Linux-ia64-MPT-icc
>>>>>>>
>>>>>>>watch the actual compile command line to see if your change went
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>through.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Gengbin
>>>>>>>
>>>>>>>Michel Espinoza-Fonseca wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>It's me again. I modify the Make.charm file, and I still got an
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>error
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>>>referring to charm++.h. It's so annoying, because I feel I'm
>>>>>>>>
>>>>>>>>
>doing
>
>
>>>>>>>>something wrong. Do you have another suggestion?
>>>>>>>>Michel
>>>>>>>>
>>>>>>>>-----Original Message-----
>>>>>>>>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu] Sent: Monday,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>March
>>
>>
>>
>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>
>>>
>>>
>>>
>>>>>>>>07, 2005 2:23 PM
>>>>>>>>To: Michel Espinoza-Fonseca
>>>>>>>>Cc: namd-l_at_ks.uiuc.edu
>>>>>>>>Subject: Re: namd-l: namd on Altix
>>>>>>>>
>>>>>>>>
>>>>>>>>normally you just need root directory.
>>>>>>>>you don't need to sepcify the version directory, however, if
>>>>>>>>
>>>>>>>>
>there
>
>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>is
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>minor different,
>>>>>>>>modify the CHARMARCH in Linux-ia64-MPT-icc.arch for example.
>>>>>>>>
>>>>>>>>Gengbin
>>>>>>>>
>>>>>>>>Michel Espinoza-Fonseca wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>Hi again. I have another question. Do I have to set the root
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>directory
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>where charm is installed (for example, the unzipped directory of
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>the
>>>
>>>
>>>
>>>
>>>
>>>
>>>>>>>>precompiled version)? I was trying to do this when compiling
>>>>>>>>
>>>>>>>>
>NAMD,
>
>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>but
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>it didn't work. Perhaps I'm doing something wrong.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>Sorry for the inconveniences.
>>>>>>>>>Cheers,
>>>>>>>>>Michel
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>-----Original Message-----
>>>>>>>>>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu]
>>>>>>>>>Sent: Mon 3/7/2005 1:39 PM
>>>>>>>>>To: Michel Espinoza-Fonseca
>>>>>>>>>Cc: namd-l_at_ks.uiuc.edu
>>>>>>>>>Subject: Re: namd-l: namd on Altix
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>You can refer to the NAMD notes.txt on how to compile NAMD. For
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>that
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>>error, you need to config NAMD Make.charm to tell NAMD where
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>Charm
>>
>>
>>
>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>
>>>
>>>
>>>
>>>>>>>>>is installed.
>>>>>>>>>
>>>>>>>>>Gengbin
>>>>>>>>>
>>>>>>>>>Michel Espinoza-Fonseca wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>Thank you for your reply. Actually I don't have any problem
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>compiling
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>>>charm, but when I try to build NAMD, simply it doesn't work. I
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>remember
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>>that appears something like "charm++.h not found". So I don't
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>know...
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>>>Michel
>>>>>>>>>>
>>>>>>>>>>-----Original Message-----
>>>>>>>>>>From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu] Sent: Monday,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>March
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>>>07, 2005 1:34 PM
>>>>>>>>>>To: Michel Espinoza-Fonseca
>>>>>>>>>>Cc: namd-l_at_ks.uiuc.edu
>>>>>>>>>>Subject: Re: namd-l: namd on Altix
>>>>>>>>>>
>>>>>>>>>>Michel Espinoza-Fonseca wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>Hi all,
>>>>>>>>>>>
>>>>>>>>>>>Does anybody have compiled NAMD on Altix (i64 proc.). I was
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>trying
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>to
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>>>compile it, without success. It'll be very useful for me if
>>>>>>>>>>>somebody can provide the namd exe for this system.
>>>>>>>>>>>
>>>>>>>>>>>Thank you very much!
>>>>>>>>>>>
>>>>>>>>>>>Cheers,
>>>>>>>>>>>
>>>>>>>>>>>Michel
>>>>>>>>>>>
>>>>>>>>>>>L. Michel Espinoza-Fonseca
>>>>>>>>>>>
>>>>>>>>>>>BSBI, UMN
>>>>>>>>>>>
>>>>>>>>>>>mef_at_ddt.biochem.umn.edu
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>You can download the latest charm at:
>>>>>>>>>>http://charm.cs.uiuc.edu/autobuild/cur
>>>>>>>>>>
>>>>>>>>>>You can even try the pre-compiled version look for
>>>>>>>>>>mpi-linux-ia64-ifort-mpt-icc
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>><http://charm.cs.uiuc.edu/autobuild/cur/mpi-linux-ia64-ifort-mpt-ic
>>>>>>
>>>>>>
>c
>
>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>.
>>
>>
>>
>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>t
>>>
>>>
>>>
>>>
>>>
>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>xt
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>>To compile charm, use:
>>>>>>>>>>./build charm++ mpi-linux-ia64 mpt icc ifort
>>>>>>>>>>
>>>>>>>>>>Gengbin
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:13 CST