RE: namd on Altix

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Mar 07 2005 - 18:43:25 CST

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/inc
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-mpt
-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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