install errors

[ben-8878]

mkdir: cannot create directory ‘build’: File exists gcc -I/home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include -g -w -c /home/yunbin .zhang/eesen/tools/ATLAS/build/..//CONFIG/src/atlconf_misc.cgcc -I/home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include -g -w -o xconfig /hom e/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/src/config.c atlconf_misc.o /tmp/cc8nyqqd.o: In function ATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use oftmpnam' is dangerous, better use mkstemp'./xconfig -d s /home/yunbin.zhang/eesen/tools/ATLAS/build/../ -d b /home/yunbin.zhang/eese n/tools/ATLAS/build probe_OS.o: In functionATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use of tmpnam' is dangerous, better usemkstemp' OS configured as Linux (1) probe_asm.o: In function ATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use oftmpnam' is dangerous, better use mkstemp' Assembly configured as GAS_x8664 (2) probe_vec.o: In functionATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use of tmpnam' is dangerous, better usemkstemp' Vector ISA Extension configured as SSE3 (6,448) probe_arch.o: In function ATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use oftmpnam' is dangerous, better use mkstemp' Architecture configured as PII (18) /tmp/ccpW77vq.o: In functionATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use of tmpnam' is dangerous, better usemkstemp' Clock rate configured as 2399Mhz

Maximum number of threads configured as 28 probe_pmake.o: In function ATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use oftmpnam' is dangerous, better use mkstemp'Parallel make command configured as '$(MAKE) -j 28' Cannot detect CPU throttling. gcc -I/home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include -g -w -o xisgcc /home /yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/src/IsGcc.c atlconf_misc.o /tmp/cc2IakgI.o: In functionATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use of tmpnam' is dangerous, better usemkstemp'gcc -I/home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include -g -w -c /home/yunbin .zhang/eesen/tools/ATLAS/build/..//CONFIG/src/probe_comp.cgcc -I/home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include -g -w -o xprobe_comp probe_comp.o atlconf_misc.o probe_comp.o: In function ATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use oftmpnam' is dangerous, better use mkstemp'rm -f config1.out make atlas_run atldir=/home/yunbin.zhang/eesen/tools/ATLAS/build exe=xprobe_comp redir=con fig1.out \ args="-v 0 -o atlconf.txt -O 1 -A 18 -Si nof77 0 -V 448 -b 64 -d b /home /yunbin.zhang/eesen/tools/ATLAS/build"make[1]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build' cd /home/yunbin.zhang/eesen/tools/ATLAS/build ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 18 -Si nof77 0 -V 448 -b 64 -d b /home/yunbin.zhang/eesen/tools/ATLAS/build > config1.outprobe_f2c.o: In function ATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use oftmpnam' is dangerous, better use mkstemp'make[1]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build' cat config1.out REPORTED: res=/usr/lib/gcc/x86_64-redhat-linux/4.8.5/libgfortran.so

gcc -I/home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include -g -w -o xspew /home/ yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/src/SpewMakeInc.c atlconf_misc.o \
/tmp/ccvLxI9G.o: In function ATL_tmpnam': /home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: th e use oftmpnam' is dangerous, better use mkstemp'rm -f *core* *.o config?.out 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/yunbin.zhang/eesen/tools/ATLAS/build' make -f Make.top leafstart leaf=interfaces/lapack/C2F/src make[2]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build' cd interfaces/lapack/C2F/src ; ln -s /home/yunbin.zhang/eesen/tools/ATLAS/build/Make.inc M ake.incln: failed to create symbolic link ‘Make.inc’: File exists make[2]: *** [leafstart] Error 1 make[2]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build' make[1]: [startup] Error 2 make[1]: Leaving directory `/home/yunbin.zhang/eesen/tools/ATLAS/build' make: [startup] Error 2 DONE configure make -f Make.top build make[1]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build' cd bin/ ; make xatlas_build make[2]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build/bin' make[2]: xatlas_build' is up to date. make[2]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build/bin' cd bin/ ; ./xatlas_build -1 0 -a 1 -l 1 make[2]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/bin' make[2]: *** No rule to make target/home/yunbin.zhang/eesen/tools/ATLAS/build/..//CONFIG /ARCHS/PII64SSE3.tar.bz2', needed by /home/yunbin.zhang/eesen/tools/ATLAS/build/ARCHS/PII64SSE3'. Stop.make[2]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build/bin'

BEGIN STAGE 1-0-0: SYSTEM PROBE/AUX COMPILE at 10:21 make[2]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/bin' cd /home/yunbin.zhang/eesen/tools/ATLAS/build/src/auxil ; make -s ATL_buildinfo.o cd /home/yunbin.zhang/eesen/tools/ATLAS/build/src/auxil ; make lib make[3]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build/src/auxil' cd /home/yunbin.zhang/eesen/tools/ATLAS/build/src/blas/level1 ; make lib make[4]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/blas/level1' make dgen make[5]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build/src/blas/level1' make Make_drot make[6]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/blas/level1' cd /home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1 ; make dinstall_rot make[7]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1' rm -f GEN/* ./xrotsrch -p d TST: make drottest urout=rot1_x0y0.c opt=" -X 4 1 -1 2 -3 -Y 4 1 -1 3 -2" make[8]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1' cd /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing ; make lib make[8]: *** read jobs pipe EOF. Stop. make[8]: *** Waiting for unfinished jobs.... make[9]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make -j 28 dlib.grd make[9]: read jobs pipe EOF. Stop. make[9]: Waiting for unfinished jobs.... make[10]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[10]: warning: -jN forced in submake: disabling jobserver mode. make[10]:dlib.grd' is up to date. make[10]: Leaving directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[9]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[8]: [tstlib.grd] Error 2 make[8]: Leaving directory /home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1' TST: make drottest urout=rot1_x1y1.c opt="" make[8]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1' cd /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing ; make lib make[8]: read jobs pipe EOF. Stop. make[8]: Waiting for unfinished jobs.... make[9]: Entering directory `/home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make -j 28 dlib.grd make[9]: read jobs pipe EOF. Stop. make[9]: Waiting for unfinished jobs.... make[10]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[10]: warning: -jN forced in submake: disabling jobserver mode. make[10]:dlib.grd' is up to date. make[10]: Leaving directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[9]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[8]: [tstlib.grd] Error 2 make[8]: Leaving directory /home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1' TST: make drottest urout=rot4_x1y1.c opt="" make[8]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1' cd /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing ; make lib make[8]: read jobs pipe EOF. Stop. make[8]: Waiting for unfinished jobs.... make[9]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make -j 28 dlib.grd make[9]: *** read jobs pipe EOF. Stop. make[9]: *** Waiting for unfinished jobs.... make[10]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[10]: warning: -jN forced in submake: disabling jobserver mode. make[10]: dlib.grd' is up to date. make[10]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[9]: Leaving directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/testing' make[8]: *** [tstlib.grd] Error 2 make[8]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1' NO GENERAL CASE SURVIVED!! ABORTING!! ID incX incY alpha beta ROUT ==== ==== ==== ===== ==== ============= 1 0 0 2 2 rot1_x0y0.c 2 1 1 2 2 rot1_x1y1.c 3 1 1 2 2 rot4_x1y1.c

make[7]: [dinstall_rot] Error 255 make[7]: Leaving directory `/home/yunbin.zhang/eesen/tools/ATLAS/build/tune/blas/level1' make[6]: [Make_drot] Error 2 make[6]: Leaving directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/blas/level1' make[5]: *** [dgen] Error 2 make[5]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build/src/blas/level1' make[4]: [dlib] Error 2 make[4]: Leaving directory `/home/yunbin.zhang/eesen/tools/ATLAS/build/src/blas/level1' make[3]: [lib.grd] Error 2 make[3]: Leaving directory /home/yunbin.zhang/eesen/tools/ATLAS/build/src/auxil' make[2]: *** [IStage1] Error 2 make[2]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build/bin' ERROR 621 DURING CACHESIZE SEARCH!!. CHECK INSTALL_LOG/Stage1.log FOR DETAILS. make[2]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build/bin' cd /home/yunbin.zhang/eesen/tools/ATLAS/build ; make error_report make[3]: Entering directory/home/yunbin.zhang/eesen/tools/ATLAS/build' make -f Make.top error_report make[4]: Entering directory /home/yunbin.zhang/eesen/tools/ATLAS/build' uname -a 2>&1 >> bin/INSTALL_LOG/ERROR.LOG /usr/bin/gcc -v 2>&1 >> bin/INSTALL_LOG/ERROR.LOG Using built-in specs. COLLECT_GCC=/usr/bin/gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/i nfo --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linuxThread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-16) (GCC) /usr/bin/gcc -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOG gcc: error: unrecognized command line option ‘-V’ gcc: fatal error: no input files compilation terminated. make[4]: [error_report] Error 4 (ignored) /usr/bin/gcc --version 2>&1 >> bin/INSTALL_LOG/ERROR.LOG tar cf error_PII64SSE3.tar Make.inc bin/INSTALL_LOG/* bzip2 error_PII64SSE3.tar bzip2: Output file error_PII64SSE3.tar.bz2 already exists. make[4]: *** [error_report] Error 1 make[4]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build' make[3]: [error_report] Error 2 make[3]: Leaving directory `/home/yunbin.zhang/eesen/tools/ATLAS/build' make[2]: [error_report] Error 2 make[2]: Leaving directory /home/yunbin.zhang/eesen/tools/ATLAS/build/bin' cat: ../../CONFIG/error.txt: No such file or directory cat: ../../CONFIG/error.txt: No such file or directory make[1]: *** [build] Error 255 make[1]: Leaving directory/home/yunbin.zhang/eesen/tools/ATLAS/build' make: *** [build] Error 2

[fmetze]

This looks like a problem when building ATLAS? Hard to debug without any extra information. I would create a clean environment (new checkout) and try to run without parallelization (not use make -j)

[ben-8878]

yes, when i run install_atlas.sh,met the error.

[riebling]

A work-around might be to install Atlas system-wide, such as with a package manager,

sudo apt-get install libatlas3-base libatlas-base-dev libatlas-dev

(This is how we provision virtual machines that install Eesen - but requires root privileges)

[ben-8878]

I want to make sure that my operation is correct？ cd tools sudo yum install libatlas3-base libatlas-base-dev libatlas-dev but still exist some errors, otherwisse, my linux system is redhat not ubuntu. errors are as # follows: [root@node1 tools]# sudo yum install libatlas3-base libatlas-base-dev libatlas-dev Loaded plugins: fastestmirror, langpacks epel | 4.3 kB 00:00:00
erlang-solutions | 951 B 00:00:00
extras | 2.9 kB 00:00:00
msxf | 2.9 kB 00:00:00
nux-dextop | 2.9 kB 00:00:00
nvidia-diag-driver-local-384.66 | 2.4 kB 00:00:00
os | 3.6 kB 00:00:00
updates | 2.9 kB 00:00:00
Loading mirror speeds from cached hostfile

• nux-dextop: li.nux.ro No package libatlas3-base available. No package libatlas-base-dev available. No package libatlas-dev available. Error: Nothing to do

[riebling]

ok sorry, I gave instructions specific to Ubuntu. Not sure of the Atlas package names on RedHat

[kidconan]

I want to make sure that my operation is correct？ cd tools sudo yum install libatlas3-base libatlas-base-dev libatlas-dev but still exist some errors, otherwisse, my linux system is redhat not ubuntu. errors are as # follows: [root@node1 tools]# sudo yum install libatlas3-base libatlas-base-dev libatlas-dev Loaded plugins: fastestmirror, langpacks epel | 4.3 kB 00:00:00 erlang-solutions | 951 B 00:00:00 extras | 2.9 kB 00:00:00 msxf | 2.9 kB 00:00:00 nux-dextop | 2.9 kB 00:00:00 nvidia-diag-driver-local-384.66 | 2.4 kB 00:00:00 os | 3.6 kB 00:00:00 updates | 2.9 kB 00:00:00 Loading mirror speeds from cached hostfile

• nux-dextop: li.nux.ro No package libatlas3-base available. No package libatlas-base-dev available. No package libatlas-dev available. Error: Nothing to do

Hey, have you solved this question? And what's your enviroment? centos7? Now I meet the same difficulty in installing EESEN? If you succed, could you tell how to solve it.

[fmetze]

closed for inactivity