Hi All,
I am getting an gcc error while installing lxml of python version 2.7 and
3.6.6. Both are showing same error.
eb lxml-4.2.5-foss-2018b-Python-2.7.15.eb -dr
== temporary log file in case of crash
/tmp/jobs/snow/7052/eb-Lbjbnl/easybuild-s4Wtql.log
== resolving dependencies ...
== processing EasyBuild easyconfig
/sNow/easybuild/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.0-py2.7.egg/easybuild/easyconfigs/l/lxml/lxml-4.2.5-foss-2018b-Python-2.7.15.eb
== building and installing lxml/4.2.5-foss-2018b-Python-2.7.15...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== FAILED: Installation ended unsuccessfully (build directory:
/sNow/easybuild/centos/7.3.1611/Broadwell/build/lxml/4.2.5/foss-2018b-Python-2.7.15):
build failed (first 300 chars): cmd " pip install
--prefix=/sNow/easybuild/centos/7.3.1611/Broadwell/software/lxml/4.2.5-foss-2018b-Python-2.7.15
--no-deps --ignore-installed --no-build-isolation ." exited with exit
code 1 and output:
Processing
/sNow/easybuild/centos/7.3.1611/Broadwell/build/lxml/4.2.5/foss-2018b-Python-2.7.1
== Results of the build can be found in the log file(s)
/sNow/easybuild/tmp/easybuild-lxml-4.2.5-20190510.025351.rnflr.log
ERROR: Build of
/sNow/easybuild/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.0-py2.7.egg/easybuild/easyconfigs/l/lxml/lxml-4.2.5-foss-2018b-Python-2.7.15.eb
failed (err: 'build failed (first 300 chars): cmd " pip install
--prefix=/sNow/easybuild/centos/7.3.1611/Broadwell/software/lxml/4.2.5-foss-2018b-Python-2.7.15
--no-deps --ignore-installed --no-build-isolation ." exited with exit
code 1 and output:\nProcessing
/sNow/easybuild/centos/7.3.1611/Broadwell/build/lxml/4.2.5/foss-2018b-Python-2.7.1')
Log details are given below
sources/xsl/iso-schematron-xslt1
copying
src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/readme.txt ->
build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1
running build_ext
building 'lxml.etree' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
creating build/temp.linux-x86_64-2.7/src/lxml
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O2
-ftree-vectorize -march=native -fno-math-errno
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/libxml2/2.9.8-GCCcore-7.3.0/include
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/libxslt/1.1.32-GCCcore-7.3.0/include
-fPIC -DCYTHON_CLINE_IN_TRACEBACK=0
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/libxslt/1.1.32-GCCcore-7.3.0/include
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-Isrc -Isrc/lxml/includes
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include/python2.7
-c src/lxml/etree.c -o build/temp.linux-x86_64-2.7/src/lxml/etree.o -w
gcc: internal compiler error: Killed (program cc1)
Please submit a full bug report,
with preprocessed source if appropriate.
See <https://gcc.gnu.org/bugs/> for instructions.
Compile failed: command 'gcc' failed with exit status 4
creating tmp
creating tmp/jobs
creating tmp/jobs/snow
creating tmp/jobs/snow/7052
creating tmp/jobs/snow/7052/eb-Lbjbnl
cc
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/libxslt/1.1.32-GCCcore-7.3.0/include
-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I/usr/include/libxml2 -c
/tmp/jobs/snow/7052/eb-Lbjbnl/xmlXPathInitMacq6q.c -o
tmp/jobs/snow/7052/eb-Lbjbnl/xmlXPathInitMacq6q.o
/tmp/jobs/snow/7052/eb-Lbjbnl/xmlXPathInitMacq6q.c:2:1: warning: return
type defaults to 'int' [-Wimplicit-int]
main (int argc, char **argv) {
^~~~
cc tmp/jobs/snow/7052/eb-Lbjbnl/xmlXPathInitMacq6q.o
-L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libxslt/1.1.32-GCCcore-7.3.0/lib
-L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libxml2/2.9.8-GCCcore-7.3.0/lib
-lxml2 -o a.out
error: command 'gcc' failed with exit status 4
----------------------------------------
Command
"/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/bin/python
-u -c "import setuptools,
tokenize;__file__='/tmp/jobs/snow/7052/eb-Lbjbnl/pip-req-build-oT8D1Q/setup.py';f=getattr(tokenize,
'open', open)(__file__);code=f.read().replace('\r\n',
'\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
/tmp/jobs/snow/7052/eb-Lbjbnl/pip-record-Yd_lFs/install-record.txt
--single-version-externally-managed --prefix
/sNow/easybuild/centos/7.3.1611/Broadwell/software/lxml/4.2.5-foss-2018b-Python-2.7.15
--compile" failed with error code 1 in
/tmp/jobs/snow/7052/eb-Lbjbnl/pip-req-build-oT8D1Q/
You are using pip version 10.0.1, however version 19.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(at
easybuild/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_framework-3.9.0-py2.7.egg/easybuild/tools/run.py:501
in parse_cmd_output)
== 2019-05-10 02:54:58,952 easyblock.py:3010 WARNING build failed (first
300 chars): cmd " pip install
--prefix=/sNow/easybuild/centos/7.3.1611/Broadwell/software/lxml/4.2.5-foss-2018b-Python-2.7.15
--no-deps --ignore-installed --no-build-isolation ." exited with exit
code 1 and output:
Processing
/sNow/easybuild/centos/7.3.1611/Broadwell/build/lxml/4.2.5/foss-2018b-Python-2.7.1
== 2019-05-10 02:54:58,952 easyblock.py:293 INFO Closing log for
application name lxml version 4.2.5
With Regards,
Sona
