Installation issue: E4S project: AML will not install on Ascent (ORNL) with gcc/6.4.0 #18196
Closed as not planned
Description
The issue appears to be a problem in the AML code itself where they are copying files to a directory that wasn't created.
This was discovered while trying to address packages that did not build for the E4S project initially. I have a suggested fix but am looking for advice on what is the best strategy. The fix is to add a mkdir command to the doc directory Makefile.am file:
$ diff -Naur aml-0.1.0/doc/Makefile.am aml-0.1.0-fixed/doc/Makefile.am
--- aml-0.1.0/doc/Makefile.am 1969-12-31 19:00:01.000000000 -0500
+++ aml-0.1.0-fixed/doc/Makefile.am 2020-08-10 17:57:57.756347000 -0400
@@ -16,6 +16,7 @@
install-doc-html: build-docs
if [ -d $(SPHINX_BUILD_DIR) ]; then \
+ mkdir -p $(DATA_INSTALL_DIR)/html \
cp -r $(SPHINX_BUILD_DIR) $(DATA_INSTALL_DIR)/html; \
fi
Because this is in the project code itself, should this fix be done by the project team responsible for aml or another option is to patch the file. Patching the file will not take effect unless we do the autogen.sh command and perhaps just patch Makefile.in which is regenerated by the autogen.sh. Does anyone have advice on how this could be done effectively?
To recreate the original problem:
spack -e . install --no-cache
with this spack.yaml file in your spack top-level directory:
spack:
packages:
all:
providers:
mpi: [spectrum-mpi]
target: [ppc64le]
buildable: true
version: []
paths: {}
modules: {}
compiler: []
cuda:
buildable: false
version: [10.1.243]
modules:
[email protected]: cuda/10.1.243
target: []
providers: {}
paths: {}
compiler: []
spectrum-mpi:
buildable: false
version:
- 10.3.1.2
modules:
[email protected]: spectrum-mpi/10.3.1.2-20200121
target: []
providers: {}
paths: {}
compiler: []
gcc:
version:
- 6.4.0
buildable: true
target: []
providers: {}
paths: {}
modules: {}
compiler: []
specs:
- aml
# - faodel
# - flecsi+cinch
# - petsc
# - turbine
# - unifyfs
config:
misc_cache: $spack/cache
install_tree: $spack/$padding:512
view: false
concretization: separately
Here is the original failed output:
==> Installing aml
==> aml: Executing phase: 'autoreconf'
==> aml: Executing phase: 'configure'
==> aml: Executing phase: 'build'
==> aml: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 2:
'make' '-j16' 'install'
4 errors found in build log:
362 mkdir -p /autofs/nccsopen-svm1_home/jgalarowicz/luke_assignment/spa
ck/spack_path_placeholder/spack_path_placeholder/spack_path_placeho
lder/spack_path_placeholder/spack_path_placeholder/spack_path_place
holder/spack_path_placeholder/spack_path_placeholder/spack_path_pla
ceholder/spack_path_placeholder/spack_path_placeholder/spack_path_p
laceholder/spack_path_placeholder/spack_path_placeholder/spack_path
_placeholder/spack_path_placeholder/spack_path_placeholder/spack_pa
th_placeholder/spack_path_placeholder/spack_path_placeholder/spack_
path_placeholder/spack_path_placeholder/spack_/linux-rhel7-ppc64le/
gcc-6.4.0/aml-0.1.0-xlnakyzomp5n6relmtb6ajb2ijrds3uz/share/aml
363 echo "not building documentation"
364 not building documentation
365 if [ -d ./build-sphinx ]; then \
366 cp -r ./build-sphinx /autofs/nccsopen-svm1_home/jgalarowicz/luke_as
signment/spack/spack_path_placeholder/spack_path_placeholder/spack_
path_placeholder/spack_path_placeholder/spack_path_placeholder/spac
k_path_placeholder/spack_path_placeholder/spack_path_placeholder/sp
ack_path_placeholder/spack_path_placeholder/spack_path_placeholder/
spack_path_placeholder/spack_path_placeholder/spack_path_placeholde
r/spack_path_placeholder/spack_path_placeholder/spack_path_placehol
der/spack_path_placeholder/spack_path_placeholder/spack_path_placeh
older/spack_path_placeholder/spack_path_placeholder/spack_/linux-rh
el7-ppc64le/gcc-6.4.0/aml-0.1.0-xlnakyzomp5n6relmtb6ajb2ijrds3uz/sh
are/aml/html; \
367 fi
>> 368 cp: cannot create directory '/autofs/nccsopen-svm1_home/jgalarowicz
/luke_assignment/spack/spack_path_placeholder/spack_path_placeholde
r/spack_path_placeholder/spack_path_placeholder/spack_path_placehol
der/spack_path_placeholder/spack_path_placeholder/spack_path_placeh
older/spack_path_placeholder/spack_path_placeholder/spack_path_plac
eholder/spack_path_placeholder/spack_path_placeholder/spack_path_pl
aceholder/spack_path_placeholder/spack_path_placeholder/spack_path_
placeholder/spack_path_placeholder/spack_path_placeholder/spack_pat
h_placeholder/spack_path_placeholder/spack_path_placeholder/spack_/
linux-rhel7-ppc64le/gcc-6.4.0/aml-0.1.0-xlnakyzomp5n6relmtb6ajb2ijr
ds3uz/share/aml/html': No such file or directory
>> 369 make[2]: *** [install-doc-html] Error 1
370 make[2]: *** Waiting for unfinished jobs....
371 make[2]: Leaving directory `/autofs/nccsopen-svm1_home/jgalarowicz/
tempspack/spack-stage/spack-stage-aml-0.1.0-xlnakyzomp5n6relmtb6ajb
2ijrds3uz/spack-src/doc'
>> 372 make[1]: *** [install-am] Error 2
373 make[1]: Leaving directory `/autofs/nccsopen-svm1_home/jgalarowicz/
tempspack/spack-stage/spack-stage-aml-0.1.0-xlnakyzomp5n6relmtb6ajb
2ijrds3uz/spack-src/doc'
>> 374 make: *** [install-recursive] Error 1
See build log for details:
/ccsopen/home/jgalarowicz/tempspack/spack-stage/spack-stage-aml-0.1.0-xlnakyzomp5n6relmtb6ajb2ijrds3uz/spack-build-out.txt