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Unable to compile ATLAS 3.10.1
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Jim Petersen



Joined: 26 Feb 2013
Posts: 6

PostPosted: Wed Feb 27, 2013 10:46 am    Post subject: Unable to compile ATLAS 3.10.1 Reply with quote

I am trying to compile ATLAS 3.10.1 using the instructions at http://www.pgroup.com/resources/atlas/atlas3932_pgi2010.htm. I follow the steps outlined to step 4, which is where I run the configure utility, which compiles the programs. At this point, the system fails. It seems that it first fails when it cannot find features.h. I would appreciate any suggesions.

Here is the output:

jn_petersen@chebe-gpu:~/atlas/ATLAS3.10.1/my_build_dir$ ../configure -C ic pgcc -F ic "-O2" -C if pgf77 -F if "-O2" --with-netlib-lapack-tarfile=/home/jn_petersen/numerics/lapack.gz
make: `xconfig' is up to date.
./xconfig -d s /home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir/../ -d b /home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir -C ic pgcc -F ic -O2 -C if pgf77 -F if -O2 -Si lapackref 1

OS configured as Linux (1)

Assembly configured as GAS_x8664 (2)

Vector ISA Extension configured as AVX (5,480)

Architecture configured as Corei2 (26)

Clock rate configured as 2001Mhz

Maximum number of threads configured as 24
Parallel make command configured as '$(MAKE) -j 24'
Cannot detect CPU throttling.
rm -f config1.out
make atlas_run atldir=/home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir exe=xprobe_comp redir=config1.out \
args="-v 0 -o atlconf.txt -O 1 -A 26 -Si nof77 0 -V 480 -C ic 'pgcc' -F ic '-O2' -C if 'pgf77' -F if '-O2' -b 64 -d b /home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir"
make[1]: Entering directory `/home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir'
cd /home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 26 -Si nof77 0 -V 480 -C ic 'pgcc' -F ic '-O2' -C if 'pgf77' -F if '-O2' -b 64 -d b /home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir > config1.out
sh: 2: Syntax error: EOF in backquote substitution
sh: 2: Syntax error: EOF in backquote substitution
sh: 2: Syntax error: EOF in backquote substitution
PGC-F-0206-Can't find include file bits/predefs.h (/usr/include/features.h: 324)
PGC/x86-64 Linux 13.2-0: compilation aborted
make[2]: *** [IRunCComp] Error 2


Unable to find usable compiler for ICC; abortingMake sure compilers are in your path, and specify good compilers to configure
(see INSTALL.txt or 'configure --help' for details)make[1]: *** [atlas_run] Error 1
make[1]: Leaving directory `/home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir'
make: *** [IRun_comp] Error 2
ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 0 -o atlconf.txt -O 1 -A 26 -Si nof77 0 -V 480 -C ic 'pgcc' -F ic '-O2' -C if 'pgf77' -F if '-O2' -b 64"'
mkdir src bin tune interfaces
mkdir: cannot create directory `src': File exists
mkdir: cannot create directory `bin': File exists
mkdir: cannot create directory `tune': File exists
mkdir: cannot create directory `interfaces': File exists
make: *** [make_subdirs] Error 1
make -f Make.top startup
make[1]: Entering directory `/home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir'
Make.top:1: Make.inc: No such file or directory
Make.top:325: warning: overriding commands for target `/AtlasTest'
Make.top:76: warning: ignoring old commands for target `/AtlasTest'
make[1]: *** No rule to make target `Make.inc'. Stop.
make[1]: Leaving directory `/home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir'
make: *** [startup] Error 2
mv: cannot stat `lib/Makefile': No such file or directory
../configure: 450: ../configure: cannot create lib/Makefile: Directory nonexistent
../configure: 451: ../configure: cannot create lib/Makefile: Directory nonexistent
../configure: 452: ../configure: cannot create lib/Makefile: Directory nonexistent
../configure: 453: ../configure: cannot create lib/Makefile: Directory nonexistent
../configure: 509: ../configure: cannot create lib/Makefile: Directory nonexistent
DONE configure
jn_petersen@chebe-gpu:~/atlas/ATLAS3.10.1/my_build_dir$
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mkcolg



Joined: 30 Jun 2004
Posts: 6215
Location: The Portland Group Inc.

PostPosted: Wed Feb 27, 2013 12:38 pm    Post subject: Reply with quote

Hi Jim,

I just tried configuring ATLAS 3.10 with PGI 13.2 on my system, and it was fine. It seem so me to be some OS header file issue the following:
Quote:
PGC-F-0206-Can't find include file bits/predefs.h (/usr/include/features.h: 324)


What OS are you using? Are you able to compile a simple C program with pgcc?

I was able to find one system running Ubuntu 12.04 that had a "/usr/include/features.h" header file that contained an include of predefs.h at line 324. However, ATLAS configure correctly and predefs.h exists in "/usr/include/bits".

- Mat
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Jim Petersen



Joined: 26 Feb 2013
Posts: 6

PostPosted: Wed Feb 27, 2013 2:42 pm    Post subject: Reply with quote

I am using Ubuntu 12.04.2. i have the features.h. But the system didn't have the .h file referenced here. I found that i could instiall it using (sudo apt-get install libc6-dev-i386).

It seems to have compiled. Now, when i execute the "make build" command, it is stopping with an error report. I will now seek help from the ATLAS support team, as this seems to be unrelated to PGI compilers at this stage.

Thanks.

--Jim
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Jim Petersen



Joined: 26 Feb 2013
Posts: 6

PostPosted: Thu Feb 28, 2013 6:58 am    Post subject: Problem compiling ATLAS with PGI compilers Reply with quote

While attempting to install ATLAS, the "make build" step stops at the following:

/opt/pgi/linux86-64/13.2/bin/pgcc -fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2 -mavx -m64 -x assembler-with-cpp -DL2SIZE=4194304 -I/home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir/include -I/home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir/..//include -I/home/jn_petersen/atlas/ATLAS3.10.1/my_build_dir/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_Corei2 -DATL_CPUMHZ=2001 -DATL_AVX -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -m64 -DATL_FULL_LAPACK -DATL_NCPU=24 -DDREAL -o ATL_dset_xp1yp0aXbX.o -c ATL_dset_xp1yp0aXbX.c
pgcc-Error-Unknown switch: -fomit-frame-pointer
pgcc-Error-Unknown switch: -mfpmath=sse
pgcc-Error-Unknown switch: -fno-schedule-insns2
pgcc-Error-Unknown switch: -mavx
pgcc-Error-Unknown switch: -x
make[6]: *** [ATL_dset_xp1yp0aXbX.o] Error 1

These options work with gcc, but not with the pgcc compiler. Consequently, there seems to be an incompatibility between ATLAS and the pgi compilers.

Suggestions?
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mkcolg



Joined: 30 Jun 2004
Posts: 6215
Location: The Portland Group Inc.

PostPosted: Thu Feb 28, 2013 11:25 am    Post subject: Reply with quote

Hi Jim,

I've tried multiple option to ATLAS's configure script, but it seems that they have hard coded "gcc" and some of it's options into the build. I was able to work around the error you're seeing by setting all the "-F" options (i.e. xc, gc, sk, dk, etc.) to "-O2", but later in the build a "-x " flag is added which we don't recognize. I tried adding our "-noswitcherror" to have pgcc ignore flags it doesn't recognize, but I then get a syntax error later in the build.

Unfortunately, I'm not sure how to work around these issues and would recommend you use gcc instead of pgcc since that what ATLAS 3.10 is expecting.

Code:
../configure -C if pgf77 -F if "-O2" --with-netlib-lapack-tarfile=/home/jn_petersen/numerics/lapack.gz


- Mat
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