From 5e8fa56223bedc4934ac969e42775a8c758b8bc5 Mon Sep 17 00:00:00 2001 From: Fabio Roberto Vitello Date: Wed, 29 Apr 2020 12:35:00 +0200 Subject: [PATCH 1/5] Updated DDF2 Dependencies - Added Lofar Beam to base image - changed killMS version to the private one - Added bootstrap cats from https://www.ict.inaf.it/gitlab/lofarit/container-data.git - ddf container now run as root --- .DS_Store | Bin 0 -> 10244 bytes base/Dockerfile | 3 ++- base/entrypoint.sh | 2 +- ddf2/Dockerfile | 24 ++++++++++++++++-------- 4 files changed, 19 insertions(+), 10 deletions(-) create mode 100644 .DS_Store diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..fe5ea3ce7a1e7fc318c5d8176e3830d61b978af7 GIT binary patch literal 10244 zcmeHMO>h)N6n<|BFf)MZK=@gT#R(xP0ueWV@>9fYHc=`H650GgAjxcIAfuC+xHFp# zgkY+?Sc+O6{6oF?TUI=2>CIBgimz7wg;e$y2kS+LQS;xy#|KrQ7r9vVg z5s(N-1SA3yf$ISQ%Gtaq%Y>A*L_i`S5tv1Qe;;(ZxJ*TITFCIzK~=Z~AX!4{uuz-v z21z}VsYp%>Nh4HHxRMmE7;Q07xRYLw>{5}O7E-taMw<_eX2xiTg5m6Re?2q@ObID# ziGW1las>EmQvz8qzz1vo{yjV9*nW^qev7e1C5x9VRaE+|P>yCsyh0{0g1nzLa{av5 zX#^wLsNLmx&TQMr_SjZokd?Q2ZeZB1l?$D1(;|~2y|!z5g|wGYpPbCtV`~!tJNDDZkw7?m9T3)(`%LB{gFbe0>RK~MO95z8C?14@=1SS;V3_Jx-!%Hv&Z^L`=A$$&Bz?bkfT!0_p zXZRIRj6YPZpCf515?7+1Jct?W!XE5L6D>T3Bj{oQC-4ML z;zM`_AH&D-Nj!@$<16?ozK-wW`}hH#!%y&2{06_rAH+IiMY`@6{bG$5sWtmP5?!P7 zwAjFv=$g25ua^E->H6Jr&e5`!tIAhztlV--{f<4YvyXAXlbcVXkT-%DAz_My2p`|2 zETrchU$1RQbQ7!1OBFo;dG)}V@Tht1^l}z``&=J z;2eAgUlHpr!cXuE{Dwe`W4H!465lFtGgjetOky22U?VnT3vn-vZMYBb!2@_N@vk3` z;s6ezf%l<gv2-Jvu-?- za~;n;PCCxg5_)?~I0p6q-RuwrD6<1)7MUHc`|L1BSD77TcDPpAA!6Nv>>v_|tR(^x zfg25hMPk7^KmWhu>i_@WXkp3qN(3YV{{R6jY0tE$$)R{CvCx;Fwd-^Z(Zvh5n-(&3 zq3V)90;t2!6~i+b8jH@hLcbL0x&O3~p*!_McaqoW&j7jq=kU)Kx&IFjIR01r|Gxo; C^7$ /opt/DDFacet/init.sh +RUN cd /opt && git clone https://www.ict.inaf.it/gitlab/lofarit/container-data.git -USER lofar +#USER lofar ENV CONTAINER_NAME='ddf2_base3.10' +ENV DDF_PIPELINE_CATALOGS='/opt/container-data/bootstrap-cats/' -- GitLab From c63c243f10622d5509855a0ab556645a3133858f Mon Sep 17 00:00:00 2001 From: Fabio Roberto Vitello Date: Tue, 5 May 2020 10:51:05 +0200 Subject: [PATCH 2/5] Update Dockerfile Added missing emcee --- ddf2/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ddf2/Dockerfile b/ddf2/Dockerfile index 9dede8f..e2ad608 100644 --- a/ddf2/Dockerfile +++ b/ddf2/Dockerfile @@ -32,7 +32,7 @@ COPY DDFacet /opt/DDFacet RUN cp /opt/ddf-pipeline/misc/setup.cfg /opt/DDFacet/ # Fix compile options RUN python -m pip install -U pip setuptools wheel RUN pip install -U pip setuptools wheel -RUN python -m pip install numpy==1.16 bdsf==1.8.15 +RUN python -m pip install numpy==1.16 bdsf==1.8.15 emcee RUN python -m pip install pybind11 future pyregion sshtunnel pymysql psutil RUN python -m pip install -U "/opt/DDFacet/[dft-support,moresane-support,testing-requirements,fits-beam-support]" -- GitLab From dc091b5480890fff592fe0e94646eab6565071cb Mon Sep 17 00:00:00 2001 From: Fabio Roberto Vitello Date: Sun, 24 May 2020 11:36:27 +0200 Subject: [PATCH 3/5] Updated numpy to 1.16.6 The pipeline was crashing due a numpy error that is fixed in version >1.16. meqtrees_cattery was not happy with numpy > 1.16 due his specification: pkg_resources.ContextualVersionConflict: (numpy 1.16.6), Requirement.parse('numpy<=1.16'), set(['meqtrees-cattery'])) Edited Dockerfile to change the version on the METADATA --- .gitignore | 3 +++ ddf2/Dockerfile | 6 ++++-- 2 files changed, 7 insertions(+), 2 deletions(-) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..c0ff1e7 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ + +ddf2/DDFacet/ +ddf2/killMS/ diff --git a/ddf2/Dockerfile b/ddf2/Dockerfile index e2ad608..b5e3989 100644 --- a/ddf2/Dockerfile +++ b/ddf2/Dockerfile @@ -32,16 +32,18 @@ COPY DDFacet /opt/DDFacet RUN cp /opt/ddf-pipeline/misc/setup.cfg /opt/DDFacet/ # Fix compile options RUN python -m pip install -U pip setuptools wheel RUN pip install -U pip setuptools wheel -RUN python -m pip install numpy==1.16 bdsf==1.8.15 emcee +RUN python -m pip install numpy==1.16.6 bdsf==1.8.15 emcee RUN python -m pip install pybind11 future pyregion sshtunnel pymysql psutil RUN python -m pip install -U "/opt/DDFacet/[dft-support,moresane-support,testing-requirements,fits-beam-support]" RUN cd /opt/DDFacet && rm -rf /opt/DDFacet/Dcbuild && python setup.py build -RUN python -m pip install bdsf==1.8.15 +RUN python -m pip install bdsf==1.8.15 numpy==1.16.6 RUN sed -e "s|INSTALLDIR|/opt|" /opt/ddf-pipeline/misc/DDF.sh > /opt/DDFacet/init.sh +RUN sed 's/numpy (<=1.16)/numpy (<=1.16.6)/g' /usr/local/lib/python2.7/dist-packages/meqtrees_cattery-1.7.0.dist-info/METADATA > /usr/local/lib/python2.7/dist-packages/meqtrees_cattery-1.7.0.dist-info/METADATA + RUN cd /opt && git clone https://www.ict.inaf.it/gitlab/lofarit/container-data.git #USER lofar -- GitLab From f0706320bca459d2950117e1ea9291dbc2683498 Mon Sep 17 00:00:00 2001 From: Fabio Roberto Vitello Date: Mon, 25 May 2020 09:55:43 +0200 Subject: [PATCH 4/5] Update Dockerfile Downgraded numpy to 1.16.2 --- ddf2/Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ddf2/Dockerfile b/ddf2/Dockerfile index b5e3989..d70552c 100644 --- a/ddf2/Dockerfile +++ b/ddf2/Dockerfile @@ -32,17 +32,17 @@ COPY DDFacet /opt/DDFacet RUN cp /opt/ddf-pipeline/misc/setup.cfg /opt/DDFacet/ # Fix compile options RUN python -m pip install -U pip setuptools wheel RUN pip install -U pip setuptools wheel -RUN python -m pip install numpy==1.16.6 bdsf==1.8.15 emcee +RUN python -m pip install numpy==1.16.2 bdsf==1.8.15 emcee RUN python -m pip install pybind11 future pyregion sshtunnel pymysql psutil RUN python -m pip install -U "/opt/DDFacet/[dft-support,moresane-support,testing-requirements,fits-beam-support]" RUN cd /opt/DDFacet && rm -rf /opt/DDFacet/Dcbuild && python setup.py build -RUN python -m pip install bdsf==1.8.15 numpy==1.16.6 +RUN python -m pip install bdsf==1.8.15 numpy==1.16.2 RUN sed -e "s|INSTALLDIR|/opt|" /opt/ddf-pipeline/misc/DDF.sh > /opt/DDFacet/init.sh -RUN sed 's/numpy (<=1.16)/numpy (<=1.16.6)/g' /usr/local/lib/python2.7/dist-packages/meqtrees_cattery-1.7.0.dist-info/METADATA > /usr/local/lib/python2.7/dist-packages/meqtrees_cattery-1.7.0.dist-info/METADATA +RUN sed 's/numpy (<=1.16)/numpy (<=1.16.2)/g' /usr/local/lib/python2.7/dist-packages/meqtrees_cattery-1.7.0.dist-info/METADATA > /usr/local/lib/python2.7/dist-packages/meqtrees_cattery-1.7.0.dist-info/METADATA RUN cd /opt && git clone https://www.ict.inaf.it/gitlab/lofarit/container-data.git -- GitLab From 97392dc803a46f48ea48ce6d51b78806dc05819c Mon Sep 17 00:00:00 2001 From: Fabio Roberto Vitello Date: Fri, 5 Jun 2020 12:18:54 +0200 Subject: [PATCH 5/5] Updated Dockerfile Added astropy_healpix --- ddf2/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ddf2/Dockerfile b/ddf2/Dockerfile index d70552c..8d7a589 100644 --- a/ddf2/Dockerfile +++ b/ddf2/Dockerfile @@ -34,7 +34,7 @@ RUN python -m pip install -U pip setuptools wheel RUN pip install -U pip setuptools wheel RUN python -m pip install numpy==1.16.2 bdsf==1.8.15 emcee -RUN python -m pip install pybind11 future pyregion sshtunnel pymysql psutil +RUN python -m pip install astropy_healpix pybind11 future pyregion sshtunnel pymysql psutil RUN python -m pip install -U "/opt/DDFacet/[dft-support,moresane-support,testing-requirements,fits-beam-support]" RUN cd /opt/DDFacet && rm -rf /opt/DDFacet/Dcbuild && python setup.py build -- GitLab