Hi Sage Developers,
I'm trying to install Sage on multiple computers in a network to run my
code simultaneously on all of them. At CU, all of the department computers
share a filesystem but might have different versions of RedHat Linux or
different dependencies installed. I just tried to install and build Sage
from source on one of these computers and got an error during the 'make'.
I've attached the log file and would like help to get Sage working
correctly. My next question is about running the same installation from
other computers. Do you know if that will work? under specific
conditions? Do I need to 'make' Sage for each computer that I want to use
it on?
If I can give you any extra information, please let me know.
Thanks,
Amy
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atlas-3.8.4.p1
Machine:
Linux dotdot.colorado.edu 2.6.18-308.el5 #1 SMP Fri Jan 27 17:21:15 EST 2012 i686 i686 i386 GNU/Linux
Deleting directories from past builds of previous/current versions of atlas-3.8.4.p1
Extracting package /home/student/keighley/sage-4.8/spkg/standard/atlas-3.8.4.p1.spkg ...
-rw-r--r-- 1 keighley student 2867171 Jan 15 07:16 /home/student/keighley/sage-4.8/spkg/standard/atlas-3.8.4.p1.spkg
Finished extraction
****************************************************
Host system
uname -a:
Linux dotdot.colorado.edu 2.6.18-308.el5 #1 SMP Fri Jan 27 17:21:15 EST 2012 i686 i686 i386 GNU/Linux
****************************************************
****************************************************
CC Version
gcc -v
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --disable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=i386-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-52)
****************************************************
Configuration:
SAGE_LOCAL: /home/student/keighley/sage-4.8/local
linker_Solaris?: False
PPC?: False
SPKG_DIR: /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1
linker_GNU?: True
ld: GNU
system: Linux
Darwin?: False
machine: i686
fortran: gfortran
Solaris?: False
fortran_g95?: False
bits: 32bit
CYGWIN?: False
SPARC?: False
fortran_GNU?: True
FreeBSD?: False
32bit?: True
IA64?: False
Linux?: True
64bit?: False
Intel?: True
processor: i686
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/student/keighley/sage-4.8/local --with-netlib-lapack=/home/student/keighley/sage-4.8/local/lib/liblapack.a --ccmake[2]: Entering directory `/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build'
make[2]: Warning: File `Makefile' has modification time 1.5 s in the future
gcc -I/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/include -g -w -c /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/src/atlconf_misc.c
gcc -I/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/include -g -w -o xconfig /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/src/config.c atlconf_misc.o
atlconf_misc.o: In function `CmndResults':
/home/student/keighley/sage-4.8/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]: warning: Clock skew detected. Your build may be incomplete.
make[2]: Leaving directory `/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build'
./xconfig -d s /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src/ -d b /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build -Ss flapack /home/student/keighley/sage-4.8/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 32 -O 1
make[2]: Warning: File `Makefile' has modification time 1.3 s in the future
atlconf_misc.o: In function `CmndResults':
/home/student/keighley/sage-4.8/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[3]: Warning: File `Makefile' has modification time 1.2 s in the future
make[3]: warning: Clock skew detected. Your build may be incomplete.
make[2]: warning: Clock skew detected. Your build may be incomplete.
make[2]: Warning: File `Makefile' has modification time 1.1 s in the future
atlconf_misc.o: In function `CmndResults':
/home/student/keighley/sage-4.8/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[3]: Warning: File `Makefile' has modification time 0.94 s in the future
make[3]: warning: Clock skew detected. Your build may be incomplete.
make[2]: warning: Clock skew detected. Your build may be incomplete.
make[2]: Warning: File `Makefile' has modification time 0.48 s in the future
atlconf_misc.o: In function `CmndResults':
/home/student/keighley/sage-4.8/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[3]: Warning: File `Makefile' has modification time 0.36 s in the future
make[4]: Warning: File `Makefile' has modification time 0.35 s in the future
make[5]: Warning: File `Makefile' has modification time 0.24 s in the future
make[5]: warning: Clock skew detected. Your build may be incomplete.
make[4]: warning: Clock skew detected. Your build may be incomplete.
make[3]: warning: Clock skew detected. Your build may be incomplete.
make[2]: warning: Clock skew detected. Your build may be incomplete.
make[2]: Warning: File `Makefile' has modification time 0.21 s in the future
make[3]: Warning: File `Makefile' has modification time 0.2 s in the future
make[4]: Warning: File `Makefile' has modification time 0.19 s in the future
make[5]: Warning: File `Makefile' has modification time 0.18 s in the future
make[5]: warning: Clock skew detected. Your build may be incomplete.
make[4]: warning: Clock skew detected. Your build may be incomplete.
make[4]: Warning: File `Makefile' has modification time 0.16 s in the future
atlconf_misc_BE.o: In function `CmndResults':
/home/student/keighley/sage-4.8/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[4]: warning: Clock skew detected. Your build may be incomplete.
make[3]: warning: Clock skew detected. Your build may be incomplete.
make[2]: warning: Clock skew detected. Your build may be incomplete.
make[2]: Warning: File `xprobe_arch' has modification time 0.93 s in the future
make[4]: Warning: File `xarchinfo_x86' has modification time 0.9 s in the future
make[4]: warning: Clock skew detected. Your build may be incomplete.
make[4]: Warning: File `xarchinfo_linux' has modification time 1.9 s in the future
make[4]: warning: Clock skew detected. Your build may be incomplete.
make[2]: warning: Clock skew detected. Your build may be incomplete.
atlconf_misc.o: In function `CmndResults':
/home/student/keighley/sage-4.8/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]: Warning: File `xprobe_arch' has modification time 0.69 s in the future
make[4]: Warning: File `xarchinfo_x86' has modification time 0.67 s in the future
make[4]: warning: Clock skew detected. Your build may be incomplete.
make[4]: Warning: File `xarchinfo_linux' has modification time 1.6 s in the future
make[4]: warning: Clock skew detected. Your build may be incomplete.
make[2]: warning: Clock skew detected. Your build may be incomplete.
It appears you have cpu throttling enabled, which makes timings
unreliable and an ATLAS install nonsensical. Aborting.
See ATLAS/INSTALL.txt for further information
Ignoring CPU throttling by user override!
make[2]: Entering directory `/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build'
gcc -I/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/include -g -w -c /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/src/probe_comp.c
gcc -I/home/student/keighley/sage-4.8/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/student/keighley/sage-4.8/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/student/keighley/sage-4.8/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 32" \
redir=config1.out
make[3]: Entering directory `/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build'
cd /home/student/keighley/sage-4.8/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 32 > config1.out
cc1: error: unrecognized command line option "-mavx"
/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/src/backend/comptestC.c:1: warning: SSE instruction set disabled, using 387 arithmetics
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/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build'
make[2]: *** [IRun_comp] Error 2
make[2]: Leaving directory `/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build'
xconfig: /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src//CONFIG/src/config.c:125: ProbeComp: Assertion `!system(ln)' failed.
Assembly configured as GAS_x8632 (1)
Vector ISA Extension configured as SSE3 (2,28)
Architecture configured as Corei2 (19)
Clock rate configured as 1600Mhz
Maximum number of threads configured as 4
Parallel make command configured as '$(MAKE) -j 4'
CPU Throttling apparently enabled!
/bin/sh: line 1: 3194 Aborted ./xconfig -d s /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build/../src/ -d b /home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1/ATLAS-build -Ss flapack /home/student/keighley/sage-4.8/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 32 -O 1
xconfig exited with 134
="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 32 -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 0m3.305s
user 0m1.338s
sys 0m1.126s
************************************************************************
Error installing package atlas-3.8.4.p1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/home/student/keighley/sage-4.8/spkg/logs/atlas-3.8.4.p1.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/home/student/keighley/sage-4.8/spkg/build/atlas-3.8.4.p1' && '/home/student/keighley/sage-4.8/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
