5.2 does not compile, breaks in atlas

[jyr]

Hi,

Just tried to compile 5.2 on a RHEL 5.8 system on the latest HP
ProLiant ml110 G7 system and the compile breaks while trying to
configure and compile atlas.

I have downloaded the latest version of atlas3.10.0.tar.bz2 and that
compiles out of the box on its own. The original version of
atlas3.8.4.tar.bz2 equally does not compile.

some output:


****************************************************
Host system:
Linux ml110g7 2.6.18-308.11.1.el5 #1 SMP Fri Jun 15 15:41:53 EDT 2012
x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/home/jr/software/sage/sage-5.1/local/libexec/gcc/
x86_64-unknown-linux-gnu/4.6.3/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../src/configure --prefix=/home/jr/software/sage/
sage-5.1/local --with-local-prefix=/home/jr/software/sage/sage-5.1/
local --with-gmp=/home/jr/software/sage/sage-5.1/local --with-mpfr=/
home/jr/software/sage/sage-5.1/local --with-mpc=/home/jr/software/sage/
sage-5.1/local --with-system-zlib --disable-multilib
Thread model: posix
gcc version 4.6.3 (GCC)
****************************************************
Configuration:
SAGE_LOCAL: /home/jr/software/sage/sage-5.1/local
linker_Solaris?: False
PPC?: False
SPKG_DIR: /home/jr/software/sage/sage-5.1/spkg/build/
atlas-3.8.4.p1
linker_GNU?: True
ld: GNU
system: Linux
Darwin?: False
machine: x86_64
fortran: gfortran
Solaris?: False
fortran_g95?: False
bits: 64bit
CYGWIN?: False
SPARC?: False
fortran_GNU?: True
FreeBSD?: False
32bit?: False
IA64?: False
Linux?: True
64bit?: True
Intel?: True
processor: x86_64
Copying patches/Make.top to src
Copying patches/archinfo_linux.c to src/CONFIG/src/backend/
archinfo_linux.c
Copying patches/archinfo_x86.c to src/CONFIG/src/backend/
archinfo_x86.c
Copying patches/probe_comp.c to src/CONFIG/src/probe_comp.c
First attempt: automatic tuning.
Running configure with arch = None and isa extensions None
Running ../src/configure --prefix=/home/jr/software/sage/sage-5.1/
local --with-netlib-lapack=/home/jr/software/sage/sage-5.1/local/lib/
liblapack.a make[2]: Entering directory `/home/jr/software/sage/
sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-build'
gcc -I/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/include -g -w -c /home/jr/software/sage/sage-5.1/
spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/src/
atlconf_misc.c
gcc -I/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/include -g -w -o xconfig /home/jr/software/sage/
sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/src/
config.c atlconf_misc.o
atlconf_misc.o: In function `CmndResults':
/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/src/atlconf_misc.c:306: warning: the use of
`tmpnam' is dangerous, better use `mkstemp'
make[2]: Leaving directory `/home/jr/software/sage/sage-5.1/spkg/build/
atlas-3.8.4.p1/ATLAS-build'
./xconfig -d s /home/jr/software/sage/sage-5.1/spkg/build/
atlas-3.8.4.p1/ATLAS-build/../src/ -d b /home/jr/software/sage/
sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-build -Ss flapack /home/jr/
software/sage/sage-5.1/local/lib/liblapack.a -Si cputhrchk 0 -Fa alg -
fPIC -C if sage_fortran -C xc gcc -C ic gcc -C dm gcc -C sm gcc -C dk
gcc -C sk gcc -b 64 -O 1
atlconf_misc.o: In function `CmndResults':
/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/src/atlconf_misc.c:306: warning: the use of
`tmpnam' is dangerous, better use `mkstemp'
atlconf_misc.o: In function `CmndResults':
/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/src/atlconf_misc.c:306: warning: the use of
`tmpnam' is dangerous, better use `mkstemp'
atlconf_misc.o: In function `CmndResults':
/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/src/atlconf_misc.c:306: warning: the use of
`tmpnam' is dangerous, better use `mkstemp'
atlconf_misc_BE.o: In function `CmndResults':
/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/src/atlconf_misc.c:306: warning: the use of
`tmpnam' is dangerous, better use `mkstemp'
atlconf_misc.o: In function `CmndResults':
/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/src/atlconf_misc.c:306: warning: the use of
`tmpnam' is dangerous, better use `mkstemp'
make[2]: Entering directory `/home/jr/software/sage/sage-5.1/spkg/
build/atlas-3.8.4.p1/ATLAS-build'
gcc -I/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/include -g -w -c /home/jr/software/sage/sage-5.1/
spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/src/probe_comp.c
gcc -I/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/include -g -w -o xprobe_comp probe_comp.o
atlconf_misc.o
atlconf_misc.o: In function `CmndResults':
/home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build/../src//CONFIG/src/atlconf_misc.c:306: warning: the use of
`tmpnam' is dangerous, better use `mkstemp'
rm -f config1.out
make -j1 atlas_run atldir=/home/jr/software/sage/sage-5.1/spkg/build/
atlas-3.8.4.p1/ATLAS-build exe=xprobe_comp args="-v 0 -o atlconf.txt -
O 1 -A 19 -Si nof77 0 -C ic 'gcc' -Fa ic '-fPIC' -C sm 'gcc' -Fa sm '-
fPIC' -C dm 'gcc' -Fa dm '-fPIC' -C sk 'gcc' -Fa sk '-fPIC' -C dk
'gcc' -Fa dk '-fPIC' -C xc 'gcc' -Fa xc '-fPIC' -C if 'sage_fortran' -
Fa if '-fPIC' -b 64" \
redir=config1.out
make[3]: Entering directory `/home/jr/software/sage/sage-5.1/spkg/
build/atlas-3.8.4.p1/ATLAS-build'
cd /home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 19 -Si nof77 0 -C
ic 'gcc' -Fa ic '-fPIC' -C sm 'gcc' -Fa sm '-fPIC' -C dm 'gcc' -Fa dm
'-fPIC' -C sk 'gcc' -Fa sk '-fPIC' -C dk 'gcc' -Fa dk '-fPIC' -C xc
'gcc' -Fa xc '-fPIC' -C if 'sage_fortran' -Fa if '-fPIC' -b 64 >
config1.out
as: unrecognized option `-msse2avx'
make[4]: *** [IRunCComp] Error 1


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[3]: ***
[atlas_run] Error 1
make[3]: Leaving directory `/home/jr/software/sage/sage-5.1/spkg/build/
atlas-3.8.4.p1/ATLAS-build'
make[2]: *** [IRun_comp] Error 2
make[2]: Leaving directory `/home/jr/software/sage/sage-5.1/spkg/build/
atlas-3.8.4.p1/ATLAS-build'
xconfig: /home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/
ATLAS-build/../src//CONFIG/src/config.c:125: ProbeComp: Assertion `!
system(ln)' failed.

Assembly configured as GAS_x8664 (2)

Vector ISA Extension configured as SSE3 (2,28)

Architecture configured as Corei2 (19)

Clock rate configured as 3093Mhz

Maximum number of threads configured as 4
Parallel make command configured as '$(MAKE) -j 4'
Cannot detect CPU throttling.
/bin/sh: line 1: 24754 Aborted ./xconfig -d s /home/jr/
software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src/ -
d b /home/jr/software/sage/sage-5.1/spkg/build/atlas-3.8.4.p1/ATLAS-
build -Ss flapack /home/jr/software/sage/sage-5.1/local/lib/
liblapack.a -Si cputhrchk 0 -Fa alg -fPIC -C if sage_fortran -C xc gcc
-C ic gcc -C dm gcc -C sm gcc -C dk gcc -C sk gcc -b 64 -O 1
xconfig exited with 134
--cc="gcc" -Si cputhrchk 0 -Fa alg -fPIC -C if sage_fortran -C xc
"gcc" -C ic "gcc" -C dm "gcc" -C sm "gcc" -C dk "gcc" -C sk "gcc" -b
64 -O 1
Traceback (most recent call last):
File "./spkg-install", line 442, in <module>
rc = build()
File "./spkg-install", line 431, in build
assert rc==0, 'Configure failed!'
AssertionError: Configure failed!

real 0m1.421s
user 0m0.913s
sys 0m0.488s
************************************************************************
Error installing package atlas-3.8.4.p1
************************************************************************