From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Sun Dec 07 2008 - 23:16:42 CST
Hello all. I have successfully compiled two seperate 64bit versions
of NAMD (actually one is a pseudo-64bit) for Intel Xeon Macs. I did
two builds with the following pieces:
Pseudo 64 bit=
-Latest source dump of charm++ compiled twice (once as 32bit and the
other as 64 bit)
-Bleeding edge NAMD
-Precompiled 32bit Intel Mac versions of TCL and FFTW (8.4 and 2.1,
-I did a "make" on the NAMD using the 32 pieces as a 32bit compile
using the CFLAGS=-O3 -arch x86 -fexpensive-optimizations -fomit-frame-
pointer -ffast-math -fno-strict-aliasing
-Then I took the 64bit charmrun and replaced the 32bit charmrun that
was in the folder with namd2, etc.
Full 64 bit=
-Latest source dump of charm++ compiled only as 64bit Intel
-Bleeding edge NAMD
-I compiled 64 bit TCL8.5 using ./configure --disable-shared --
enable-64bit --disable-corefoundation CFLAGS="-O3 -D_NO_STRING_INLINES
-I compiled 64 bit FFTW2.1 using ./configure --enable-float --enable-
type-prefix CFLAGS="-O3 -arch x86_64"
-I did a "make" on the NAMD using the 64 pieces as a 64bit compile
using the CFLAGS=-O3 -arch x86_64 -fexpensive-optimizations -fomit-
frame-pointer -ffast-math -fno-strict-aliasing
After running the two to check performance, I noticed the following on
the same initial simulation and same computer over 300 total steps each:
Original precompiled NAMD download for Mac Intel 32bit---1.05/step
Pseudo 64 bit (half 32bit/half64bit)---0.73/step
Full 64 bit--------0.77/step
The pseudo 64bit is faster then my fully 64bit. Which is certainly
possible, but I think it is probably something else. The only
difference between the builds are the following:
Pseudo uses precompiled binaries with CFLAGS that are potentially
different then mine because I have know idea which were used when
whomever made them, made them.
Full is using TCL8.5 not 8.4.
My questions are the following:
1) Is there any reason why TCL8.5 would be a problem versus 8.4 that
anyone knows of?
2) Can anyone tell me what the configure and/or the CFLAGS were on
those precompiled binaries for Mac Intel of FFTW and TCL8.4? I would
like to repeat with the same flags (with the exception of -arch
x86_64) in order to see if that is the main problem.
3) Can anyone tell me if there is any flag above that would cause any
problems for either the NAMD or the other makes?
Finally, I have to note that when running the make on the full 64bit
version during the compiling of most files that had to do with TCL I
got the following warning (usually many times over):
src/<X>tcl.C Warning: deprecated conversion from string constant to
char* where <X> was a different name each time (eg. X=globalmaster).
Thanks for all the input thus far and for any more to come.
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