Update docs to 2.6.1

Author: vasdommes

.circleci/config.yml

@@ -7,7 +7,7 @@
 # 3. 'deploy-master': On each 'master' branch update,
 #     push the fresh image to DockerHub as '${DOCKER_USERNAME}/sdpb:master', e.g. 'davidsd/sdpb:master'
 # 4. 'deploy-tag': If new tag is pushed to the repo,
-#     push the image '${DOCKER_USERNAME}/sdpb:${TAG}', e.g. 'davidsd/sdpb:2.6.0'
+#     push the image '${DOCKER_USERNAME}/sdpb:${TAG}', e.g. 'davidsd/sdpb:2.6.1'
 #
 # Deploy works only if you specify DOCKER_USERNAME and DOCKER_PASSWORD environment variables for the CircleCI project
 # See instructions here:
@@ -134,7 +134,7 @@ workflows:
       - deploy-tag:
           filters:
             tags:
-              only: /^\d+\.\d+\.\d+$/ # only release tags, e.g 2.6.0
+              only: /^\d+\.\d+\.\d+$/ # only release tags, e.g 2.6.1
             # See https://discuss.circleci.com/t/tag-not-triggered-by-circleci-not-filter-in-workflow/32036
             branches:
               ignore: /.*/ # Ignore all branches, otherwise the job is triggered by any git push

Changelog.md

@@ -1,3 +1,16 @@
+# Version 2.6.1
+
+- Fixed major memory leak in binary SDP deserialization. See [#160](https://github.com/davidsd/sdpb/pull/160).
+- Improve debug mode output: print `MemUsed` and `MemTotal` for each node, print `max MemUsed` at the end,
+  disable `proc/self/statm`. See [#161](https://github.com/davidsd/sdpb/pull/161).
+- Refactoring: moved common headers to `sdpb_util`, simplified include paths.
+  See [#157](https://github.com/davidsd/sdpb/pull/157).
+- Updated installations
+  for [BU](docs/site_installs/Boston.md), [Caltech](docs/site_installs/Caltech.md), [Expanse](docs/site_installs/Expanse.md), [Harvard](docs/site_installs/Harvard.md),
+  and [Imperial College](docs/site_installs/Imperial.md) clusters, with example scripts.
+
+See https://github.com/davidsd/sdpb/releases/tag/2.6.1 for the full changelog.
+
 # Version 2.6.0
 
 - New **INCOMPATIBLE** format for sdp.zip.

docs/Docker.md

@@ -20,9 +20,9 @@ can be downloaded from [Docker Hub](https://hub.docker.com/r/bootstrapcollaborat
 
     docker pull bootstrapcollaboration/sdpb:master
 
-You can also download image for a specific release, e.g., 2.6.0:
+You can also download image for a specific release, e.g., 2.6.1:
 
-    docker pull bootstrapcollaboration/sdpb:2.6.0
+    docker pull bootstrapcollaboration/sdpb:2.6.1
 
 The list of all available tags can be found in
 [bootstrapcollaboration/sdpb](https://hub.docker.com/r/bootstrapcollaboration/sdpb/tags) repo on Docker Hub.

docs/SDPB_Manual/SDPB-Manual.pdf

@@ -38,7 +38,7 @@
 
 {\Large
 \begin{center}
-{\bf SDPB 2.6.0 \\\vspace{.1in}}
+{\bf SDPB 2.6.1 \\\vspace{.1in}}
 \end{center}
 }
 \begin{center}

docs/SDPB_Manual/SDPB-Manual.tex

@@ -54,21 +54,21 @@ and push it to [local registry](https://docs.docker.com/registry/):
 
 ## Run Singularity image
 Singularity should automatically mount your home directory.  If your
-Singularity image is named `sdpb-2.6.0.sif`, you can invoke the SDPB
+Singularity image is named `sdpb-2.6.1.sif`, you can invoke the SDPB
 programs by prepending the command with
 
-    singularity exec sdpb-2.6.0.sif
+    singularity exec sdpb-2.6.1.sif
 
 So to convert the XML input file at `/home/user/input.xml`, run the command
 
-    singularity exec sdpb-2.6.0.sif mpirun -n 4 pvm2sdp 1024 /home/user/input.xml /home/user/input
+    singularity exec sdpb-2.6.1.sif mpirun -n 4 pvm2sdp 1024 /home/user/input.xml /home/user/input
 
 This uses 4 cores when running pvm2sdp.  You can change that number to
 match your own machine.
 
 To find a primal-dual solution, 
 
-    singularity exec sdpb-2.6.0.sif mpirun -n 4 sdpb --precision=1024 --procsPerNode=4 -s /home/user/input
+    singularity exec sdpb-2.6.1.sif mpirun -n 4 sdpb --precision=1024 --procsPerNode=4 -s /home/user/input
 
 In theory, Singularity can be used to run jobs across multiple nodes.
 We have not been able to make that work yet.  So for large, multi-node

docs/Singularity.md

@@ -32,12 +32,12 @@ You may list all available versions via
 
 Fo example, `sdpb-master` is built from the latest [master](https://github.com/davidsd/sdpb/tree/master) branch (
 run `sdpb --version` to see commit hash, e.g. `SDPB 2.5.1-130-g88b1c9ae`),
-and `sdpb-2.6.0` is a stable [2.6.0](https://github.com/davidsd/sdpb/releases/tag/2.6.0) release.
+and `sdpb-2.6.1` is a stable [2.6.1](https://github.com/davidsd/sdpb/releases/tag/2.6.1) release.
 
 Examples below are for `sdpb-master`.
-You may replace it with another version, e.g. `sdpb-2.6.0`.
+You may replace it with another version, e.g. `sdpb-2.6.1`.
 In that case, please refer
-to [2.6.0 documentation](https://github.com/davidsd/sdpb/blob/2.6.0/docs/site_installs/Boston.md).
+to [2.6.1 documentation](https://github.com/davidsd/sdpb/blob/2.6.1/docs/site_installs/Boston.md).
 
 ## Run SDPB
 

docs/site_installs/Boston.md

@@ -33,12 +33,12 @@ You may list all available versions via
 
 Fo example, `sdpb-master` is built from the latest [master](https://github.com/davidsd/sdpb/tree/master) branch (
 run `sdpb --version` to see commit hash, e.g. `SDPB 2.5.1-130-g88b1c9ae`),
-and `sdpb-2.6.0` is a stable [2.6.0](https://github.com/davidsd/sdpb/releases/tag/2.6.0) release.
+and `sdpb-2.6.1` is a stable [2.6.1](https://github.com/davidsd/sdpb/releases/tag/2.6.1) release.
 
 Examples below are for `sdpb-master`.
-You may replace it with another version, e.g. `sdpb-2.6.0`.
+You may replace it with another version, e.g. `sdpb-2.6.1`.
 In that case, please refer
-to [2.6.0 documentation](https://github.com/davidsd/sdpb/blob/2.6.0/docs/site_installs/Caltech.md).
+to [2.6.1 documentation](https://github.com/davidsd/sdpb/blob/2.6.1/docs/site_installs/Caltech.md).
 
 ## Run SDPB
 

docs/site_installs/Caltech.md

@@ -32,12 +32,12 @@ You may list all available versions via
 
 Fo example, `sdpb-master` is built from the latest [master](https://github.com/davidsd/sdpb/tree/master) branch (
 run `sdpb --version` to see commit hash, e.g. `SDPB 2.5.1-130-g88b1c9ae`),
-and `sdpb-2.6.0` is a stable [2.6.0](https://github.com/davidsd/sdpb/releases/tag/2.6.0) release.
+and `sdpb-2.6.1` is a stable [2.6.1](https://github.com/davidsd/sdpb/releases/tag/2.6.1) release.
 
 Examples below are for `sdpb-master`.
-You may replace it with another version, e.g. `sdpb-2.6.0`.
+You may replace it with another version, e.g. `sdpb-2.6.1`.
 In that case, please refer
-to [2.6.0 documentation](https://github.com/davidsd/sdpb/blob/2.6.0/docs/site_installs/Expanse.md).
+to [2.6.1 documentation](https://github.com/davidsd/sdpb/blob/2.6.1/docs/site_installs/Expanse.md).
 
 ## Run SDPB
 

docs/site_installs/Expanse.md

@@ -32,12 +32,12 @@ You may list all available versions via
 
 Fo example, `sdpb-master` is built from the latest [master](https://github.com/davidsd/sdpb/tree/master) branch (
 run `sdpb --version` to see commit hash, e.g. `SDPB 2.5.1-130-g88b1c9ae`),
-and `sdpb-2.6.0` is a stable [2.6.0](https://github.com/davidsd/sdpb/releases/tag/2.6.0) release.
+and `sdpb-2.6.1` is a stable [2.6.1](https://github.com/davidsd/sdpb/releases/tag/2.6.1) release.
 
 Examples below are for `sdpb-master`.
-You may replace it with another version, e.g. `sdpb-2.6.0`.
+You may replace it with another version, e.g. `sdpb-2.6.1`.
 In that case, please refer
-to [2.6.0 documentation](https://github.com/davidsd/sdpb/blob/2.6.0/docs/site_installs/Harvard.md).
+to [2.6.1 documentation](https://github.com/davidsd/sdpb/blob/2.6.1/docs/site_installs/Harvard.md).
 
 ## Run SDPB