Re: namd on Altix

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Tue Mar 08 2005 - 16:54:16 CST

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-ia
>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/in
>>
>>
>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-mp
>>
>>
>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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