Re: namd on Altix

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Tue Mar 08 2005 - 17:00:05 CST

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-ia
>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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