Re: namd on Altix

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Tue Mar 08 2005 - 17:09:47 CST

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-linux-
>>>
>>>
>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-icc/
>>>>
>>>>
>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-ifort-
>>>>
>>>>
>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-icc.
>>>>
>>>>
>t
>
>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>xt
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>>To compile charm, use:
>>>>>>>>./build charm++ mpi-linux-ia64 mpt icc ifort
>>>>>>>>
>>>>>>>>Gengbin
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>
>
>
>
>

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