Dear Sona,
On 10/05/2019 09:00, Ms. Sona CP wrote:
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.
Sometimes an ICE (internal compiler error) can happen because of memory
limits, so maybe try this in an environment that is a bit more generous
w.r.t. available memory?
Also check if setting "ulimit -s unlimited" helps at all.
regards,
Kenneth
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
