segmentation fault
Closed this issue · 2 comments
myoung3 commented
I'm getting a segmentation fault when trying to link a recent version of MKL on a recent version of rocker. I'm not sure if this is an issue with the sylabs remote builder or with the script itself and unfortunately I dont have easy access to ubuntu/debian machine with root to try locally. Can you advise? Here's my singularity .def file:
Bootstrap: docker
From: rocker/geospatial:4.1.0
Stage: build
############################################
%post
############################################
##intel mkl###
apt update
apt install -y gnupg2
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB -O - > key_stored2file
apt-key add key_stored2file
rm key_stored2file
echo "deb https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list
apt update
apt install -y intel-oneapi-mkl-2021.1.1
/opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_rt.so
update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so \
libblas.so-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_rt.so 50
update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 \
libblas.so.3-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_rt.so 50
update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so \
liblapack.so-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_rt.so 50
update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 \
liblapack.so.3-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_rt.so 50
echo "/opt/intel/lib/intel64" > /etc/ld.so.conf.d/mkl.conf
echo "/opt/intel/mkl/lib/intel64" >> /etc/ld.so.conf.d/mkl.conf
ldconfig
echo "MKL_THREADING_LAYER=GNU" >> /etc/environment
Build Log with segmentation fault error
singularity build --remote mkl.sif mkl.def
INFO: Access Token Verified!
INFO: Token stored in /root/.singularity/remote.yaml
INFO: Remote "default" now in use.
INFO: Starting build...
Getting image source signatures
Copying blob sha256:16ec32c2132b43494832a05f2b02f7a822479f8250c173d0ab27b3de78b2f058
Copying blob sha256:e031c1a9f2f8981caa2c98eccc68a7f37f276578570815a2a750f1a9a7a26a2b
Copying blob sha256:a70855d85b62f4445418b3403977c218af39b555b9d024b0e34d854b43461a73
Copying blob sha256:ee8d56356e0a287731be50c207130a0960ec541c009ac15613f895f2f2d5278e
Copying blob sha256:5d3c6fe2adc613012e5716756b9ad873b0e98761c70c1f2bbe0c0ab3c92359b4
Copying blob sha256:fc0654371b2f0535df2bda795325c8f2b561f13186a133469562b9685abc6768
Copying blob sha256:8d80cde37ed7f3a04b27909799a1e1c73fe9fafbc38699ecbc7c82d36559d6fd
Copying blob sha256:4cfc1cf5c9b8960e2c477c2273d72febaf6003d9efe46601d484f2876e1193f3
Copying config sha256:7088bb9885c96e3651bac5b55ab97ad5a39f912a837acc7fc72d261107125a21
Writing manifest to image destination
Storing signatures
2021/07/31 16:06:19 info unpack layer: sha256:16ec32c2132b43494832a05f2b02f7a822479f8250c173d0ab27b3de78b2f058
2021/07/31 16:06:20 info unpack layer: sha256:e031c1a9f2f8981caa2c98eccc68a7f37f276578570815a2a750f1a9a7a26a2b
2021/07/31 16:06:20 info unpack layer: sha256:a70855d85b62f4445418b3403977c218af39b555b9d024b0e34d854b43461a73
2021/07/31 16:06:29 info unpack layer: sha256:ee8d56356e0a287731be50c207130a0960ec541c009ac15613f895f2f2d5278e
2021/07/31 16:06:43 info unpack layer: sha256:5d3c6fe2adc613012e5716756b9ad873b0e98761c70c1f2bbe0c0ab3c92359b4
2021/07/31 16:06:43 info unpack layer: sha256:fc0654371b2f0535df2bda795325c8f2b561f13186a133469562b9685abc6768
2021/07/31 16:06:51 info unpack layer: sha256:8d80cde37ed7f3a04b27909799a1e1c73fe9fafbc38699ecbc7c82d36559d6fd
2021/07/31 16:07:10 info unpack layer: sha256:4cfc1cf5c9b8960e2c477c2273d72febaf6003d9efe46601d484f2876e1193f3
INFO: Running post scriptlet
+ apt update
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
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Fetched 18.7 MB in 2s (7,519 kB/s)
Reading package lists...
Building dependency tree...
Reading state information...
2 packages can be upgraded. Run 'apt list --upgradable' to see them.
+ apt install -y gnupg2
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
dirmngr gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client
gpg-wks-server gpgconf gpgsm libassuan0 libksba8 libnpth0 pinentry-curses
Suggested packages:
dbus-user-session libpam-systemd pinentry-gnome3 tor parcimonie xloadimage
scdaemon pinentry-doc
The following NEW packages will be installed:
dirmngr gnupg gnupg-l10n gnupg-utils gnupg2 gpg gpg-agent gpg-wks-client
gpg-wks-server gpgconf gpgsm libassuan0 libksba8 libnpth0 pinentry-curses
0 upgraded, 15 newly installed, 0 to remove and 2 not upgraded.
Need to get 2,541 kB of archives.
After this operation, 7,541 kB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu focal/main amd64 libassuan0 amd64 2.5.3-7ubuntu2 [35.7 kB]
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Get:3 http://archive.ubuntu.com/ubuntu focal/main amd64 libksba8 amd64 1.3.5-2 [92.6 kB]
Get:4 http://archive.ubuntu.com/ubuntu focal/main amd64 libnpth0 amd64 1.6-1 [7,736 B]
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Get:6 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gnupg-l10n all 2.2.19-3ubuntu2.1 [51.7 kB]
Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gnupg-utils amd64 2.2.19-3ubuntu2.1 [480 kB]
Get:8 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpg amd64 2.2.19-3ubuntu2.1 [483 kB]
Get:9 http://archive.ubuntu.com/ubuntu focal/main amd64 pinentry-curses amd64 1.1.0-3build1 [36.3 kB]
Get:10 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpg-agent amd64 2.2.19-3ubuntu2.1 [232 kB]
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Get:15 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 gnupg2 all 2.2.19-3ubuntu2.1 [4,584 B]
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Processing triggers for libc-bin (2.31-0ubuntu9.2) ...
+ wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB -O -
--2021-07-31 16:07:37-- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
Resolving apt.repos.intel.com (apt.repos.intel.com)... 184.84.65.68, 2600:1408:8400:5ac::4b23, 2600:1408:8400:58d::4b23
Connecting to apt.repos.intel.com (apt.repos.intel.com)|184.84.65.68|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3796 (3.7K) [binary/octet-stream]
Saving to: ‘STDOUT’
0K ... 100% 525M=0s
2021-07-31 16:07:38 (525 MB/s) - written to stdout [3796/3796]
+ apt-key add key_stored2file
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
+ rm key_stored2file
deb https://apt.repos.intel.com/oneapi all main
+ + tee /etc/apt/sources.list.d/oneAPI.list
echo deb https://apt.repos.intel.com/oneapi all main
+ apt update
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Hit:1 http://security.ubuntu.com/ubuntu focal-security InRelease
Get:2 https://apt.repos.intel.com/oneapi all InRelease [4,390 B]
Hit:3 http://archive.ubuntu.com/ubuntu focal InRelease
Hit:4 http://archive.ubuntu.com/ubuntu focal-updates InRelease
Hit:5 http://archive.ubuntu.com/ubuntu focal-backports InRelease
Get:6 https://apt.repos.intel.com/oneapi all/main all Packages [16.4 kB]
Get:7 https://apt.repos.intel.com/oneapi all/main amd64 Packages [84.6 kB]
Fetched 105 kB in 0s (238 kB/s)
Reading package lists...
Building dependency tree...
Reading state information...
2 packages can be upgraded. Run 'apt list --upgradable' to see them.
+ apt install -y intel-oneapi-mkl-2021.1.1
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
intel-oneapi-common-licensing intel-oneapi-common-licensing-2021.3.0
intel-oneapi-common-vars intel-oneapi-compiler-dpcpp-cpp-runtime
intel-oneapi-compiler-dpcpp-cpp-runtime-2021.3.0
intel-oneapi-compiler-shared-common-runtime-2021.3.0
intel-oneapi-compiler-shared-runtime-2021.3.0 intel-oneapi-condaindex
intel-oneapi-mkl-common-2021.1.1 intel-oneapi-openmp-2021.3.0
intel-oneapi-openmp-common-2021.3.0 intel-oneapi-tbb
intel-oneapi-tbb-2021.3.0 intel-oneapi-tbb-common-2021.3.0
The following NEW packages will be installed:
intel-oneapi-common-licensing intel-oneapi-common-licensing-2021.3.0
intel-oneapi-common-vars intel-oneapi-compiler-dpcpp-cpp-runtime
intel-oneapi-compiler-dpcpp-cpp-runtime-2021.3.0
intel-oneapi-compiler-shared-common-runtime-2021.3.0
intel-oneapi-compiler-shared-runtime-2021.3.0 intel-oneapi-condaindex
intel-oneapi-mkl-2021.1.1 intel-oneapi-mkl-common-2021.1.1
intel-oneapi-openmp-2021.3.0 intel-oneapi-openmp-common-2021.3.0
intel-oneapi-tbb intel-oneapi-tbb-2021.3.0 intel-oneapi-tbb-common-2021.3.0
0 upgraded, 15 newly installed, 0 to remove and 2 not upgraded.
Need to get 473 MB of archives.
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Get:1 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-common-licensing-2021.3.0 all 2021.3.0-261 [35.6 kB]
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Get:3 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-common-vars all 2021.3.0-261 [13.0 kB]
Get:4 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-compiler-shared-common-runtime-2021.3.0 all 2021.3.0-3350 [14.6 MB]
Get:5 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-condaindex amd64 2021.3.0-159 [675 kB]
Get:6 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-openmp-common-2021.3.0 all 2021.3.0-3350 [16.0 kB]
Get:7 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-openmp-2021.3.0 amd64 2021.3.0-3350 [120 MB]
Get:8 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-compiler-shared-runtime-2021.3.0 amd64 2021.3.0-3350 [5,851 kB]
Get:9 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-tbb-common-2021.3.0 all 2021.3.0-511 [21.5 kB]
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Get:11 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-compiler-dpcpp-cpp-runtime-2021.3.0 amd64 2021.3.0-3350 [129 MB]
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Get:13 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-mkl-common-2021.1.1 all 2021.1.1-52 [18.6 kB]
Get:14 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-tbb amd64 2021.3.0-511 [1,840 B]
Get:15 https://apt.repos.intel.com/oneapi all/main amd64 intel-oneapi-mkl-2021.1.1 amd64 2021.1.1-52 [200 MB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package intel-oneapi-common-licensing-2021.3.0.
(Reading database ... 59173 files and directories currently installed.)
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Setting up intel-oneapi-condaindex (2021.3.0-159) ...
Setting up intel-oneapi-common-vars (2021.3.0-261) ...
Setting up intel-oneapi-openmp-common-2021.3.0 (2021.3.0-3350) ...
Setting up intel-oneapi-common-licensing (2021.3.0-261) ...
Setting up intel-oneapi-mkl-common-2021.1.1 (2021.1.1-52) ...
Setting up intel-oneapi-compiler-shared-common-runtime-2021.3.0 (2021.3.0-3350) ...
Setting up intel-oneapi-tbb-common-2021.3.0 (2021.3.0-511) ...
Setting up intel-oneapi-openmp-2021.3.0 (2021.3.0-3350) ...
Setting up intel-oneapi-tbb-2021.3.0 (2021.3.0-511) ...
Setting up intel-oneapi-tbb (2021.3.0-511) ...
Setting up intel-oneapi-compiler-shared-runtime-2021.3.0 (2021.3.0-3350) ...
Setting up intel-oneapi-compiler-dpcpp-cpp-runtime-2021.3.0 (2021.3.0-3350) ...
Setting up intel-oneapi-compiler-dpcpp-cpp-runtime (2021.3.0-3350) ...
Setting up intel-oneapi-mkl-2021.1.1 (2021.1.1-52) ...
+ /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_rt.so
Segmentation fault
FATAL: While performing build: while running engine: exit status 139
FATAL: While performing build: build image size <= 0
eddelbuettel commented
Wrong repo. This is a helper script which make so promises whatsoevre w.r.t. containers, Rocker or not. Maybe talk to Intel?
FWIW I never saw the point of MKL. Much bigger size, OpenBLAS almost as fast. Good enough for me.
Can we close this?
myoung3 commented
fair enough, sorry for the issue spam