Re: [easybuild] Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)
Hi Ole, Mikael, I actually face the same issue. The actual error message is this one: configure: error: in `/usr/local/Software/build/lm3-w091/binutils/2.31.1/dummy-/binutils-2.31.1/gold': configure: error: C++ preprocessor "/lib/cpp" fails sanity check See `config.log' for more details yes checking whether compiling a cross-assembler... no checking for size_t... checking locale.h usability... make[1]: *** [configure-gold] Error 1 make[1]: *** Waiting for unfinished jobs I guess that doing: "yum install gcc-c++" would solve the issue. But I have not tested yet. But does it make sense to do that? Olivier On 20 Feb 2019, at 21:27, Mikael Öhman mailto:micket...@gmail.com>> wrote: Hi Ole, That still isn't the error; there should be the actual line, doing whatever compilation or linking, that failed. They just tend to be somewhere in middle of the huge output from the make command (even worse with parallel builds). You can put the entire log in some pastebin and someone is (probably) willing to take a look. I've built the entire 2019a toolchains on skylake server (with AVX512), without any modifications to any configs or blocks (on a virtual machine though, but all CPU features were exposed to the VM) Best regards, Mikael On Wed, Feb 20, 2019 at 8:58 PM Ole Holm Nielsen mailto:ole.h.niel...@fysik.dtu.dk>> wrote: Hi Åke, The make actually fails as shown below. There are hundreds of configure and checking lines above the lines I display, and the first make command fails as shown in the output. Can you suggest anything else to check? Are there issues with AVX512 on Skylake, and if so, how to work around it? FYI, the foss-2018a and foss-2018b toolchains have been built without problems on the Skylake node. Thanks, Ole On 20-02-2019 18:01, Åke Sandgren wrote: > That's not the real problem. > You have to look through that log and figure out what it really is. > I.e., where does the make actually fail. > > On 2/20/19 4:10 PM, Ole Holm Nielsen wrote: >> On 2/20/19 2:45 PM, Åke Sandgren wrote: >>> What is the actual error? Look in >>> /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log >> >> It's: >> >> $ tail /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log >> config.status: executing default commands >> make[1]: Leaving directory >> `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' >> make: *** [all] Error 2 >> (at easybuild/tools/run.py:501 in parse_cmd_output) >> == 2019-02-20 14:02:45,435 easyblock.py:2870 WARNING build failed (first >> 300 chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' >> make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: >> make[1]: Entering directory >> `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' >> make[1]: Nothing to be done for `all-target'. >> Configuring in ./libiberty >> Config >> == 2019-02-20 14:02:45,435 easyblock.py:288 INFO Closing log for >> application name binutils version 2.31.1 > >
Re: [easybuild] Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)
Hi Ole, That still isn't the error; there should be the actual line, doing whatever compilation or linking, that failed. They just tend to be somewhere in middle of the huge output from the make command (even worse with parallel builds). You can put the entire log in some pastebin and someone is (probably) willing to take a look. I've built the entire 2019a toolchains on skylake server (with AVX512), without any modifications to any configs or blocks (on a virtual machine though, but all CPU features were exposed to the VM) Best regards, Mikael On Wed, Feb 20, 2019 at 8:58 PM Ole Holm Nielsen wrote: > Hi Åke, > > The make actually fails as shown below. There are hundreds of configure > and checking lines above the lines I display, and the first make command > fails as shown in the output. > > Can you suggest anything else to check? Are there issues with AVX512 on > Skylake, and if so, how to work around it? > > FYI, the foss-2018a and foss-2018b toolchains have been built without > problems on the Skylake node. > > Thanks, > Ole > > > On 20-02-2019 18:01, Åke Sandgren wrote: > > That's not the real problem. > > You have to look through that log and figure out what it really is. > > I.e., where does the make actually fail. > > > > On 2/20/19 4:10 PM, Ole Holm Nielsen wrote: > >> On 2/20/19 2:45 PM, Åke Sandgren wrote: > >>> What is the actual error? Look in > >>> /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log > >> > >> It's: > >> > >> $ tail > /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log > >> config.status: executing default commands > >> make[1]: Leaving directory > >> `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' > >> make: *** [all] Error 2 > >> (at easybuild/tools/run.py:501 in parse_cmd_output) > >> == 2019-02-20 14:02:45,435 easyblock.py:2870 WARNING build failed (first > >> 300 chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' > >> make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: > >> make[1]: Entering directory > >> `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' > >> make[1]: Nothing to be done for `all-target'. > >> Configuring in ./libiberty > >> Config > >> == 2019-02-20 14:02:45,435 easyblock.py:288 INFO Closing log for > >> application name binutils version 2.31.1 > > > > >
Re: [easybuild] Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)
Hi Åke, The make actually fails as shown below. There are hundreds of configure and checking lines above the lines I display, and the first make command fails as shown in the output. Can you suggest anything else to check? Are there issues with AVX512 on Skylake, and if so, how to work around it? FYI, the foss-2018a and foss-2018b toolchains have been built without problems on the Skylake node. Thanks, Ole On 20-02-2019 18:01, Åke Sandgren wrote: That's not the real problem. You have to look through that log and figure out what it really is. I.e., where does the make actually fail. On 2/20/19 4:10 PM, Ole Holm Nielsen wrote: On 2/20/19 2:45 PM, Åke Sandgren wrote: What is the actual error? Look in /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log It's: $ tail /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log config.status: executing default commands make[1]: Leaving directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' make: *** [all] Error 2 (at easybuild/tools/run.py:501 in parse_cmd_output) == 2019-02-20 14:02:45,435 easyblock.py:2870 WARNING build failed (first 300 chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: make[1]: Entering directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' make[1]: Nothing to be done for `all-target'. Configuring in ./libiberty Config == 2019-02-20 14:02:45,435 easyblock.py:288 INFO Closing log for application name binutils version 2.31.1
Re: [easybuild] next EasyBuild conf call: Wed Feb 20th 2019 (*today*), 5pm CET
Notes on today's conf call are available at https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20190220 . Next conf call is planned for March 6th 2019, 5pm CET; join via https://umu.zoom.us/j/561463243 . regards, Kenneth On 20/02/2019 12:46, Kenneth Hoste wrote: Dear EasyBuilders, The next EasyBuild conf call is planned for Wed Feb 20th 2019 (today!), at 5pm CET. You can join the conf call via https://umu.zoom.us/j/561463243 . Current agenda: * update on next EasyBuild release (3.8.2 or 3.9.0) * updates on porting of EasyBuild framework to support Python 3 * follow-up on moving Python to GCCcore - cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7463 * Q Suggestions for additional topics are welcome (please let me know if you have any). More information on the EasyBuild conf calls is available at https://github.com/easybuilders/easybuild/wiki/Conference-calls . regards, Kenneth
Re: [easybuild] Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)
On 2/20/19 2:45 PM, Åke Sandgren wrote: What is the actual error? Look in /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log It's: $ tail /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log config.status: executing default commands make[1]: Leaving directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' make: *** [all] Error 2 (at easybuild/tools/run.py:501 in parse_cmd_output) == 2019-02-20 14:02:45,435 easyblock.py:2870 WARNING build failed (first 300 chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: make[1]: Entering directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' make[1]: Nothing to be done for `all-target'. Configuring in ./libiberty Config == 2019-02-20 14:02:45,435 easyblock.py:288 INFO Closing log for application name binutils version 2.31.1 On 2/20/19 2:18 PM, Ole Holm Nielsen wrote: I'm trying to build the foss-2019a toolchain with EB 3.8.1 on a new Intel Skylake node (40 cores + hyperthreading = 80 cores) but it fails in binutils-2.31.1.eb as shown below. I've tried to increase some system limits, but that doesn't seem to help. My current limits are: $ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) 5000 scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 3088986 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) 5000 open files (-n) 2500 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 4000 cpu time (seconds, -t) 3 max user processes (-u) 2000 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited Output from the build process: $ eb foss-2019a.eb -r == temporary log file in case of crash /tmp/eb-dyNH9x/easybuild-u8cWAg.log == resolving dependencies ... == processing EasyBuild easyconfig /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb == building and installing binutils/2.31.1... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == FAILED: Installation ended unsuccessfully (build directory: /home/modules/build/binutils/2.31.1/dummy-): build failed (first 300 chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: make[1]: Entering directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' make[1]: Nothing to be done for `all-target'. Configuring in ./libiberty Config == Results of the build can be found in the log file(s) /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log ERROR: Build of /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb failed (err: 'build failed (first 300 chars): cmd " env LIBS=\'-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64\' make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output:\nmake[1]: Entering directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1\'\nmake[1]: Nothing to be done for `all-target\'.\nConfiguring in ./libiberty\nConfig') Can anyone help me fix this issue? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark, Building 307, DK-2800 Kongens Lyngby, Denmark E-mail: ole.h.niel...@fysik.dtu.dk Homepage: http://dcwww.fysik.dtu.dk/~ohnielse/ Tel: (+45) 4525 3187 / Mobile (+45) 5180 1620
Re: [easybuild] Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)
I have binutils 2.31.1 on Skylake. It has been compiled without avx512 support though. I am not sure if that could play a role. Damian On 20.02.19, 14:46, "easybuild-requ...@lists.ugent.be on behalf of Åke Sandgren" wrote: What is the actual error? Look in /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log On 2/20/19 2:18 PM, Ole Holm Nielsen wrote: > I'm trying to build the foss-2019a toolchain with EB 3.8.1 on a new > Intel Skylake node (40 cores + hyperthreading = 80 cores) but it fails > in binutils-2.31.1.eb as shown below. I've tried to increase some > system limits, but that doesn't seem to help. My current limits are: > > $ ulimit -a > core file size (blocks, -c) 0 > data seg size (kbytes, -d) 5000 > scheduling priority (-e) 0 > file size (blocks, -f) unlimited > pending signals (-i) 3088986 > max locked memory (kbytes, -l) 64 > max memory size (kbytes, -m) 5000 > open files (-n) 2500 > pipe size(512 bytes, -p) 8 > POSIX message queues (bytes, -q) 819200 > real-time priority (-r) 0 > stack size (kbytes, -s) 4000 > cpu time (seconds, -t) 3 > max user processes (-u) 2000 > virtual memory (kbytes, -v) unlimited > file locks (-x) unlimited > > Output from the build process: > > $ eb foss-2019a.eb -r > == temporary log file in case of crash /tmp/eb-dyNH9x/easybuild-u8cWAg.log > == resolving dependencies ... > == processing EasyBuild easyconfig > /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb > > == building and installing binutils/2.31.1... > == fetching files... > == creating build dir, resetting environment... > == unpacking... > == patching... > == preparing... > == configuring... > == building... > == FAILED: Installation ended unsuccessfully (build directory: > /home/modules/build/binutils/2.31.1/dummy-): build failed (first 300 > chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' make > -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: > make[1]: Entering directory > `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' > make[1]: Nothing to be done for `all-target'. > Configuring in ./libiberty > Config > == Results of the build can be found in the log file(s) > /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log > ERROR: Build of > /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb > failed (err: 'build failed (first 300 chars): cmd " env > LIBS=\'-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64\' make -j 80 > CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output:\nmake[1]: > Entering directory > `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1\'\nmake[1]: > Nothing to be done for `all-target\'.\nConfiguring in ./libiberty\nConfig') > > Can anyone help me fix this issue? > > Thanks, > Ole > -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
Re: [easybuild] Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)
What is the actual error? Look in /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log On 2/20/19 2:18 PM, Ole Holm Nielsen wrote: > I'm trying to build the foss-2019a toolchain with EB 3.8.1 on a new > Intel Skylake node (40 cores + hyperthreading = 80 cores) but it fails > in binutils-2.31.1.eb as shown below. I've tried to increase some > system limits, but that doesn't seem to help. My current limits are: > > $ ulimit -a > core file size (blocks, -c) 0 > data seg size (kbytes, -d) 5000 > scheduling priority (-e) 0 > file size (blocks, -f) unlimited > pending signals (-i) 3088986 > max locked memory (kbytes, -l) 64 > max memory size (kbytes, -m) 5000 > open files (-n) 2500 > pipe size (512 bytes, -p) 8 > POSIX message queues (bytes, -q) 819200 > real-time priority (-r) 0 > stack size (kbytes, -s) 4000 > cpu time (seconds, -t) 3 > max user processes (-u) 2000 > virtual memory (kbytes, -v) unlimited > file locks (-x) unlimited > > Output from the build process: > > $ eb foss-2019a.eb -r > == temporary log file in case of crash /tmp/eb-dyNH9x/easybuild-u8cWAg.log > == resolving dependencies ... > == processing EasyBuild easyconfig > /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb > > == building and installing binutils/2.31.1... > == fetching files... > == creating build dir, resetting environment... > == unpacking... > == patching... > == preparing... > == configuring... > == building... > == FAILED: Installation ended unsuccessfully (build directory: > /home/modules/build/binutils/2.31.1/dummy-): build failed (first 300 > chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' make > -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: > make[1]: Entering directory > `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' > make[1]: Nothing to be done for `all-target'. > Configuring in ./libiberty > Config > == Results of the build can be found in the log file(s) > /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log > ERROR: Build of > /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb > failed (err: 'build failed (first 300 chars): cmd " env > LIBS=\'-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64\' make -j 80 > CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output:\nmake[1]: > Entering directory > `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1\'\nmake[1]: > Nothing to be done for `all-target\'.\nConfiguring in ./libiberty\nConfig') > > Can anyone help me fix this issue? > > Thanks, > Ole > -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
[easybuild] Re: Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)
I should add that binutils-2.31.1.eb builds and installs without problems on other nodes with an identical CentOS 7.6 setup, but these nodes contain older Sandy Bridge and Nehalem CPUs. /Ole On 2/20/19 2:18 PM, Ole Holm Nielsen wrote: I'm trying to build the foss-2019a toolchain with EB 3.8.1 on a new Intel Skylake node (40 cores + hyperthreading = 80 cores) but it fails in binutils-2.31.1.eb as shown below. I've tried to increase some system limits, but that doesn't seem to help. My current limits are: $ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) 5000 scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 3088986 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) 5000 open files (-n) 2500 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 4000 cpu time (seconds, -t) 3 max user processes (-u) 2000 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited Output from the build process: $ eb foss-2019a.eb -r == temporary log file in case of crash /tmp/eb-dyNH9x/easybuild-u8cWAg.log == resolving dependencies ... == processing EasyBuild easyconfig /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb == building and installing binutils/2.31.1... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == FAILED: Installation ended unsuccessfully (build directory: /home/modules/build/binutils/2.31.1/dummy-): build failed (first 300 chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: make[1]: Entering directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' make[1]: Nothing to be done for `all-target'. Configuring in ./libiberty Config == Results of the build can be found in the log file(s) /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log ERROR: Build of /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb failed (err: 'build failed (first 300 chars): cmd " env LIBS=\'-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64\' make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output:\nmake[1]: Entering directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1\'\nmake[1]: Nothing to be done for `all-target\'.\nConfiguring in ./libiberty\nConfig') Can anyone help me fix this issue? Thanks, Ole
[easybuild] Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)
I'm trying to build the foss-2019a toolchain with EB 3.8.1 on a new Intel Skylake node (40 cores + hyperthreading = 80 cores) but it fails in binutils-2.31.1.eb as shown below. I've tried to increase some system limits, but that doesn't seem to help. My current limits are: $ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) 5000 scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 3088986 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) 5000 open files (-n) 2500 pipe size(512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 4000 cpu time (seconds, -t) 3 max user processes (-u) 2000 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited Output from the build process: $ eb foss-2019a.eb -r == temporary log file in case of crash /tmp/eb-dyNH9x/easybuild-u8cWAg.log == resolving dependencies ... == processing EasyBuild easyconfig /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb == building and installing binutils/2.31.1... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == FAILED: Installation ended unsuccessfully (build directory: /home/modules/build/binutils/2.31.1/dummy-): build failed (first 300 chars): cmd " env LIBS='-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64' make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output: make[1]: Entering directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1' make[1]: Nothing to be done for `all-target'. Configuring in ./libiberty Config == Results of the build can be found in the log file(s) /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log ERROR: Build of /home/modules/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.8.1-py2.7.egg/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb failed (err: 'build failed (first 300 chars): cmd " env LIBS=\'-Wl,-rpath=/usr/lib -Wl,-rpath=/usr/lib64\' make -j 80 CFLAGS="-g -O2 -fPIC" " exited with exit code 2 and output:\nmake[1]: Entering directory `/home/modules/build/binutils/2.31.1/dummy-/binutils-2.31.1\'\nmake[1]: Nothing to be done for `all-target\'.\nConfiguring in ./libiberty\nConfig') Can anyone help me fix this issue? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark
Re: [easybuild] next EasyBuild conf call: Wed Feb 20th 2019 (*today*), 5pm CET
Oh, and of course, our scipy-stack module supports all versions of python. Maxime > > On Feb 20, 2019 at 6:46 AM, mailto:kenneth.ho...@ugent.be)> > wrote: > > > > Dear EasyBuilders, > > The next EasyBuild conf call is planned for Wed Feb 20th 2019 (today!), > at 5pm CET. > > You can join the conf call via https://umu.zoom.us/j/561463243 . > > Current agenda: > > * update on next EasyBuild release (3.8.2 or 3.9.0) > > * updates on porting of EasyBuild framework to support Python 3 > > * follow-up on moving Python to GCCcore > > - cfr. > https://github.com/easybuilders/easybuild-easyconfigs/issues/7463 > > * Q > > Suggestions for additional topics are welcome (please let me know if you > have any). > > > More information on the EasyBuild conf calls is available at > https://github.com/easybuilders/easybuild/wiki/Conference-calls . > > > regards, > > Kenneth >
Re: [easybuild] next EasyBuild conf call: Wed Feb 20th 2019 (*today*), 5pm CET
Hi Kenneth, I can’t make it to the meeting. However, reading the issue about python to gcccore, note that on Compute Canada, we have implemented solution #1, and the bundle module that we propose is based on the scipy stack (and is called scipy-stack) https://www.scipy.org/stackspec.html Maxime > > On Feb 20, 2019 at 6:46 AM, mailto:kenneth.ho...@ugent.be)> > wrote: > > > > Dear EasyBuilders, > > The next EasyBuild conf call is planned for Wed Feb 20th 2019 (today!), > at 5pm CET. > > You can join the conf call via https://umu.zoom.us/j/561463243 . > > Current agenda: > > * update on next EasyBuild release (3.8.2 or 3.9.0) > > * updates on porting of EasyBuild framework to support Python 3 > > * follow-up on moving Python to GCCcore > > - cfr. > https://github.com/easybuilders/easybuild-easyconfigs/issues/7463 > > * Q > > Suggestions for additional topics are welcome (please let me know if you > have any). > > > More information on the EasyBuild conf calls is available at > https://github.com/easybuilders/easybuild/wiki/Conference-calls . > > > regards, > > Kenneth >
[easybuild] next EasyBuild conf call: Wed Feb 20th 2019 (*today*), 5pm CET
Dear EasyBuilders, The next EasyBuild conf call is planned for Wed Feb 20th 2019 (today!), at 5pm CET. You can join the conf call via https://umu.zoom.us/j/561463243 . Current agenda: * update on next EasyBuild release (3.8.2 or 3.9.0) * updates on porting of EasyBuild framework to support Python 3 * follow-up on moving Python to GCCcore - cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7463 * Q Suggestions for additional topics are welcome (please let me know if you have any). More information on the EasyBuild conf calls is available at https://github.com/easybuilders/easybuild/wiki/Conference-calls . regards, Kenneth
Re: [easybuild] Lmod 7.8 is now available from the EPEL repository
On 2/20/19 11:35 AM, Kenneth Hoste wrote: On 20/02/2019 11:25, Ole Holm Nielsen wrote: On 2/20/19 11:19 AM, Jure Pečar wrote: On Wed, 20 Feb 2019 10:14:29 +0100 Ole Holm Nielsen wrote: Thanks to the kind Lmod maintainer (Orion Poplawski) of the Fedora/EPEL repository, the Lmod version in EPEL has been updated today from 6.6.3 to 7.8.16! Thanks also to the people who added to the Bugzilla request shown below! Good news! Any gotchas when moving from 6.6 to 7.8? Yes, it's great to finally have a modern Lmod via an RPM installation! I had one minor gotcha, namely an incompatible .modulerc file containing "hide-module zlib/1.2.8". Removing that file solved the problem. Welcome to the future! (well, Lmod 7.0 was released Nov 2016, so...) There was a substantial barrier in building one's own home-grown RPM package for Lmod :-( I certainly didn't feel knowledgeable enough to build my own, as many other sites have done it. Each Lmod RPM I've seen has been customized to very specific site setups. The people of TACC apparently don't want to provide a public RPM, which is perhaps quite understandable. So thank God for EPEL! There's a couple of other gotchas: the format/filename of the Lmod spider cache file has changed, and the internal format for module collections has changed. See also https://github.com/TACC/Lmod/blob/master/README.md#lmod-70 and https://sourceforge.net/p/lmod/mailman/message/35489261/ Thanks for the heads-up! /Ole
Re: [easybuild] Lmod 7.8 is now available from the EPEL repository
On 20/02/2019 11:25, Ole Holm Nielsen wrote: On 2/20/19 11:19 AM, Jure Pečar wrote: On Wed, 20 Feb 2019 10:14:29 +0100 Ole Holm Nielsen wrote: Thanks to the kind Lmod maintainer (Orion Poplawski) of the Fedora/EPEL repository, the Lmod version in EPEL has been updated today from 6.6.3 to 7.8.16! Thanks also to the people who added to the Bugzilla request shown below! Good news! Any gotchas when moving from 6.6 to 7.8? Yes, it's great to finally have a modern Lmod via an RPM installation! I had one minor gotcha, namely an incompatible .modulerc file containing "hide-module zlib/1.2.8". Removing that file solved the problem. Welcome to the future! (well, Lmod 7.0 was released Nov 2016, so...) There's a couple of other gotchas: the format/filename of the Lmod spider cache file has changed, and the internal format for module collections has changed. See also https://github.com/TACC/Lmod/blob/master/README.md#lmod-70 and https://sourceforge.net/p/lmod/mailman/message/35489261/ regards, Kenneth
Re: [easybuild] Lmod 7.8 is now available from the EPEL repository
On 2/20/19 11:19 AM, Jure Pečar wrote: On Wed, 20 Feb 2019 10:14:29 +0100 Ole Holm Nielsen wrote: Thanks to the kind Lmod maintainer (Orion Poplawski) of the Fedora/EPEL repository, the Lmod version in EPEL has been updated today from 6.6.3 to 7.8.16! Thanks also to the people who added to the Bugzilla request shown below! Good news! Any gotchas when moving from 6.6 to 7.8? Yes, it's great to finally have a modern Lmod via an RPM installation! I had one minor gotcha, namely an incompatible .modulerc file containing "hide-module zlib/1.2.8". Removing that file solved the problem. /Ole
Re: [easybuild] Lmod 7.8 is now available from the EPEL repository
On Wed, 20 Feb 2019 10:14:29 +0100 Ole Holm Nielsen wrote: > Thanks to the kind Lmod maintainer (Orion Poplawski) of the Fedora/EPEL > repository, the Lmod version in EPEL has been updated today from 6.6.3 > to 7.8.16! Thanks also to the people who added to the Bugzilla request > shown below! Good news! Any gotchas when moving from 6.6 to 7.8? -- Jurij Pečar HPC Engineer, IT Operations, IT Services EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany Room 13-401
[easybuild] Lmod 7.8 is now available from the EPEL repository
Thanks to the kind Lmod maintainer (Orion Poplawski) of the Fedora/EPEL repository, the Lmod version in EPEL has been updated today from 6.6.3 to 7.8.16! Thanks also to the people who added to the Bugzilla request shown below! A modern version of Lmod has been a very long-standing wish from many sites running CentOS/RHEL 7. No longer do sites need to build their own locally customized up-to-date version of Lmod, if they are satisfied with the EPEL version. Instructions for installing Lmod from EPEL is in my Wiki: https://wiki.fysik.dtu.dk/niflheim/EasyBuild_modules#install-lmod Best regards, Ole On 1/23/19 12:17 PM, Loris Bennett wrote: On Centos 7 I installed EB using the system version of Lmod (6.6.3). I have now installed Lmod 7.3 via its easyconfig. I now have the directory We could always hope that the EPEL maintainers would eventually agree to my request to update Lmod to 7.8 in EPEL, see https://bugzilla.redhat.com/show_bug.cgi?id=1651546 It might be beneficial if other sites would add arguments to my request in the Bugzilla, hoping that its priority might be increased. I have seconded your request. Cheers, Loris -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark
