AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Adam Thomas
October 16, 2003 02:35PM

The good folks at Aspen Systems were kind enough to give me an account on an opteron there so we could run some benchmarks. However getting afni to compile on the Opteron is proving a bit challenging. I started with Makefile.linux_gcc32 and have been tweaking it as needed. Some specs on the system:

[nih@opty src]$ uname -a
Linux opty 2.4.19-32mdksmp #1 SMP Tue Apr 29 09:45:45 EDT 2003 x86_64 unknown unknown GNU/Linux
[nih@opty src]$ cat /etc/redhat-release
Mandrake Linux release 9.0 (dolphin) for x86_64
[nih@opty src]$
[nih@opty src]$ gcc -v
Reading specs from /usr/lib64/gcc-lib/x86_64-mandrake-linux-gnu/3.2/specs
Configured with: ../configure --prefix=/usr --libdir=/usr/lib64 --with-slibdir=/lib --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --enable-long-long --enable-__cxa_atexit --enable-languages=c,c++,ada,f77,objc,java --host=x86_64-mandrake-linux-gnu --with-system-zlib
Thread model: posix
gcc version 3.2 (Mandrake Linux 9.0 3.2-6mdk)
[nih@opty src]$ rpm -q binutils
binutils-2.13.90.0.10-1mdk
[nih@opty src]$

And my most recent compilation error:

[nih@opty src]$ make -f Makefile.opty
/usr/bin/gcc -O3 -march=athlon -msse2 -ffast-math -mmmx -DLINUX2 -DNO_GAMMA -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -c 3dDeconvolve.c -I. -I/usr/X11R6/include -I/home/nih/usr/include
In file included from 3dDeconvolve.c:311:
Deconvolve.c:553: warning: static declaration for `student_t2p' follows non-static
Deconvolve.c:570: warning: static declaration for `fstat_t2p' follows non-static
/bin/rm -f 3dDeconvolve
/usr/bin/gcc -O2 -march=athlon -msse2 -ffast-math -mmmx -DLINUX2 -DNO_GAMMA -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -o 3dDeconvolve 3dDeconvolve.o -L. -L/usr/X11R6/lib -L/home/nih/usr/lib -L/usr/X11R6/lib64 -L/home/nih/usr/lib -lmri /home/nih/usr/lib/libXm.so -lXp -lXpm -lXext -lXmu -lXt -lSM -lICE -lX11 -lm -ldl -lc
/bin/rm -f plug_clust.so
/usr/bin/gcc -O2 -march=athlon -msse2 -ffast-math -mmmx -DLINUX2 -DNO_GAMMA -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -c plug_clust.c -I. -I/usr/X11R6/include -I/home/nih/usr/include
/usr/bin/gcc -shared -o plug_clust.so plug_clust.o
/usr/bin/ld: plug_clust.o: relocation R_X86_64_32S can not be used when making a shared object; recompile with -fPIC
plug_clust.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [plug_clust.so] Error 1
[nih@opty src]$


If anyone on the afni team is interested in logging into opty to play around I'm happy to provide the ssh key.

Thanks!
-Adam Thomas

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Subject Author Posted

afni on opteron

Adam Thomas October 16, 2003 02:35PM

Re: afni on opteron

rick reynolds October 22, 2003 03:11PM