RE: namd on Altix

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Mar 08 2005 - 15:03:49 CST

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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