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 zcmZQzU|@7AO)+F(P+(wS;9!8z0z3>@0Z1N%F(jFwA|Odd1_l9!r1Ii|q@4UD1_p+c zP`OcRGz3ONU^E0qLtr!nMnhn5g#aVOIUL*&dXyXufzc2c4FPxvfXW9@2LVJofcgv! z3=9nr8YINP$iM*Z0x&W#u)s8d`vDL&Agv%ZAgv%8q?LgY!~)BMwK6b5wK9UcAq)(R z3<6-I7{Of=5Ff0afe~yo0|O)2W(EdEh;{}>sLhO^P6)_ch;{}>uXr1w@?l^GXsk^HPgI%7ZggQj-#kV!|`? zQu524@=NnlioxbUB|!FY#tTSPSDPE@C>WVq*6Ju!8yZ*`>L{2Po7L8Ga)_%M+IlAB zR#sKl)Yi>}_y<-lFz`e8aB>y{sC0sQFsHc888Se@G#%!_8*mSDaZ7r7ars1KCgNL8&>3C7ETZE{P?n#qk0{Ad~zHN;32Fio;TiiZk=`lpPEp z4(43VBPy$;rfpzqW$$u@mych7i%VD}yezXgGbtxEGO;*0H7_MIFFmw8Go>UWDl;WD zuOu@qGqs45Q;>->Brh>H^@^Cdgn*=!qzp_KL@h!uhk!CiL}^lHVQFSbCBzO%1w~E{ zfvqtqi6yDN`6(b1Q@}Ekk_xIE9MK?g=c3fal2nK=m!zf^Cx<{{NO5LWDp(;Gm!3W+ zr$BK?c4i(#jU<<`2?wV@N@z}EQfdxZktCOeB?qT~cX%1Z+fYGUI}T1kMxBV{{M_8s zypm#wu%weS2Zz9kIFQ{wiNz)U1*v(dDG=W&NV;=yM1o`-Q&Lh>IFubUAmIlN0Zsu> zZ6e8_#9+c;!w|p_$&kWO&d|d!m0=pgB8Jrrn;G^p9A-GjaGv1;!)1mW3=bJzGQ4N_ z$?%Ke55r$ZHb#C%0Y*VaVMYZ;O-3z7ZANoO2S!ImCq@@WPsSj|V8#%}Fve)c6vkA> zG{y|ZJjQay3dTytYQ|>99>!kAKE{cRvltgME@52CxSVkt<9@~ij0YJ{GoE3*%6NlsY8k zWff%wKuHI}RgqPb6=32J*b3ol%4%~7Fmnhba)K4>aT&-8uyP8dKxB=%Ot}PDI0cF! zvKCxcvI1Z@U_W2|TFVC-V-X6$3^XPm(}i*YvN9LBkf z%NSQf(ic3{c|!Owl5q`ksw)dF%FD^mO9!>4z~U(kDGX^0M#HyufO>GWcF4?2AFUk* zeeHlquA{ZXXzf6++5wvC&}s)*6*5YXhQMeD46P7ghB#LNH2&|(z<_K1AEIiM91Vfd z5Ezyrz{uhf?BWFN?qTyGXsjJHo}K`e1Pxw*M)Mg# /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