From 89dcc777569d92d5e1205869c9e3953877f66b54 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Sun, 9 Jul 2023 12:47:53 +0200
Subject: [PATCH 1/4] adds mkl requirements for faster execution

---
 tools/superdsm/run-superdsm.py | 10 +++++-----
 tools/superdsm/superdsm.xml    |  2 ++
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/tools/superdsm/run-superdsm.py b/tools/superdsm/run-superdsm.py
index 67a4057e..18dff34f 100644
--- a/tools/superdsm/run-superdsm.py
+++ b/tools/superdsm/run-superdsm.py
@@ -13,11 +13,6 @@
 import shutil
 import tempfile
 
-import ray
-import superdsm.automation
-import superdsm.io
-import superdsm.render
-
 
 hyperparameters = [
     ('AF_scale', float),
@@ -73,6 +68,11 @@ def create_config(args):
     os.environ['OPENBLAS_NUM_THREADS'] = str(num_threads_per_process)
     os.environ['MKL_DEBUG_CPU_TYPE'] = '5'
 
+    import ray
+    import superdsm.automation
+    import superdsm.io
+    import superdsm.render
+
     ray.init(num_cpus=num_processes, log_to_driver=True)
 
     with tempfile.TemporaryDirectory() as tmpdirname:
diff --git a/tools/superdsm/superdsm.xml b/tools/superdsm/superdsm.xml
index ade35d96..0c22a5c6 100644
--- a/tools/superdsm/superdsm.xml
+++ b/tools/superdsm/superdsm.xml
@@ -4,6 +4,8 @@
         <requirement type="package" version="0.1.3">superdsm</requirement>
         <requirement type="package" version="1.6.0">ray-core</requirement>
         <requirement type="package" version="0.18.1">scikit-image</requirement>
+        <requirement type="package" version="2020.0">mkl</requirement>
+        <requirement type="package" version="*=mkl">blas</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[

From df2f06ef92bac712f0789c9c29e3af7ddda0264a Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Sun, 9 Jul 2023 12:56:54 +0200
Subject: [PATCH 2/4] moves MKL_DEBUG_CPU_TYPE env variable to xml

---
 tools/superdsm/run-superdsm.py |   1 -
 tools/superdsm/superdsm.xml    | 117 +++++++++++++++++----------------
 2 files changed, 60 insertions(+), 58 deletions(-)

diff --git a/tools/superdsm/run-superdsm.py b/tools/superdsm/run-superdsm.py
index 18dff34f..6bef2c09 100644
--- a/tools/superdsm/run-superdsm.py
+++ b/tools/superdsm/run-superdsm.py
@@ -66,7 +66,6 @@ def create_config(args):
 
     os.environ['MKL_NUM_THREADS'] = str(num_threads_per_process)
     os.environ['OPENBLAS_NUM_THREADS'] = str(num_threads_per_process)
-    os.environ['MKL_DEBUG_CPU_TYPE'] = '5'
 
     import ray
     import superdsm.automation
diff --git a/tools/superdsm/superdsm.xml b/tools/superdsm/superdsm.xml
index 0c22a5c6..f11a9a54 100644
--- a/tools/superdsm/superdsm.xml
+++ b/tools/superdsm/superdsm.xml
@@ -1,66 +1,69 @@
 <tool id="ip_superdsm" name="SuperDSM" version="0.1.3" profile="20.05">
-   <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description>
-   <requirements> 
+    <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description>
+    <requirements> 
         <requirement type="package" version="0.1.3">superdsm</requirement>
         <requirement type="package" version="1.6.0">ray-core</requirement>
         <requirement type="package" version="0.18.1">scikit-image</requirement>
         <requirement type="package" version="2020.0">mkl</requirement>
         <requirement type="package" version="*=mkl">blas</requirement>
-   </requirements>
-   <command detect_errors="aggressive">
-   <![CDATA[
-   python '$__tool_directory__/run-superdsm.py'
-   '${dataset}'
-   'cfg.json'
-   'masks.png'
-   'overlay.png'
-   $seg_border
-   \${GALAXY_SLOTS:-4}
-   #if str($config.AF_scale) != '':
-       --AF_scale '${config.AF_scale}'
-   #end if
-   #if str($config.c2f_region_analysis_min_atom_radius) != '':
-       --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
-   #end if
-   #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
-       --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
-   #end if
-   #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
-       --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
-   #end if
-   #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
-       --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
-   #end if
-   #if str($config.dsm_alpha) != '':
-       --dsm_alpha '${config.dsm_alpha}'
-   #end if
-   #if str($config.dsm_AF_alpha) != '':
-       --dsm_AF_alpha '${config.dsm_AF_alpha}'
-   #end if
-   #if str($config.global_energy_minimization_beta) != '':
-       --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
-   #end if
-   #if str($config.global_energy_minimization_AF_beta) != '':
-       --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
-   #end if
-   #if str($config.postprocess_mask_max_distance) != '':
-       --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
-   #end if
-   #if str($config.postprocess_mask_stdamp) != '':
-       --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
-   #end if
-   #if str($config.postprocess_max_norm_energy) != '':
-       --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
-   #end if
-   #if str($config.postprocess_min_contrast) != '':
-       --postprocess_min_contrast '${config.postprocess_min_contrast}'
-   #end if
-   #if str($config.postprocess_min_object_radius) != '':
-       --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
-   #end if
-   ]]>
-   </command>
-   <inputs>
+    </requirements>
+    <command detect_errors="aggressive">
+    <![CDATA[
+    python '$__tool_directory__/run-superdsm.py'
+    '${dataset}'
+    'cfg.json'
+    'masks.png'
+    'overlay.png'
+    $seg_border
+    \${GALAXY_SLOTS:-4}
+    #if str($config.AF_scale) != '':
+        --AF_scale '${config.AF_scale}'
+    #end if
+    #if str($config.c2f_region_analysis_min_atom_radius) != '':
+        --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
+    #end if
+    #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
+        --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
+    #end if
+    #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
+        --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
+    #end if
+    #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
+        --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
+    #end if
+    #if str($config.dsm_alpha) != '':
+        --dsm_alpha '${config.dsm_alpha}'
+    #end if
+    #if str($config.dsm_AF_alpha) != '':
+        --dsm_AF_alpha '${config.dsm_AF_alpha}'
+    #end if
+    #if str($config.global_energy_minimization_beta) != '':
+        --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
+    #end if
+    #if str($config.global_energy_minimization_AF_beta) != '':
+        --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
+    #end if
+    #if str($config.postprocess_mask_max_distance) != '':
+        --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
+    #end if
+    #if str($config.postprocess_mask_stdamp) != '':
+        --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
+    #end if
+    #if str($config.postprocess_max_norm_energy) != '':
+        --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
+    #end if
+    #if str($config.postprocess_min_contrast) != '':
+        --postprocess_min_contrast '${config.postprocess_min_contrast}'
+    #end if
+    #if str($config.postprocess_min_object_radius) != '':
+        --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
+    #end if
+    ]]>
+    </command>
+    <environment_variables>
+        <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable>
+    </environment_variables>
+    <inputs>
         <param name="dataset" type="data" format="tiff,png" label="Dataset" />
         <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" />
         <section name="config" title="Hyperparameters" expanded="false">

From 80d65809fd2bd8e1bc60dfec825a457b2bfcc874 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Sun, 9 Jul 2023 12:57:25 +0200
Subject: [PATCH 3/4] increments version of superdsm tool

---
 tools/superdsm/superdsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/superdsm/superdsm.xml b/tools/superdsm/superdsm.xml
index f11a9a54..32c9b2f9 100644
--- a/tools/superdsm/superdsm.xml
+++ b/tools/superdsm/superdsm.xml
@@ -1,4 +1,4 @@
-<tool id="ip_superdsm" name="SuperDSM" version="0.1.3" profile="20.05">
+<tool id="ip_superdsm" name="SuperDSM" version="0.1.3-1" profile="20.05">
     <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description>
     <requirements> 
         <requirement type="package" version="0.1.3">superdsm</requirement>

From dd4c3d7e4b9c27960e67a4c78f0c2a507a6392d9 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Fri, 3 Nov 2023 15:07:49 +0100
Subject: [PATCH 4/4] adds comments regarding MKL to superdsm.xml

---
 tools/superdsm/superdsm.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/superdsm/superdsm.xml b/tools/superdsm/superdsm.xml
index e9334958..1b898f07 100644
--- a/tools/superdsm/superdsm.xml
+++ b/tools/superdsm/superdsm.xml
@@ -11,8 +11,8 @@
         <requirement type="package" version="0.1.3">superdsm</requirement>
         <requirement type="package" version="1.6.0">ray-core</requirement>
         <requirement type="package" version="0.18.1">scikit-image</requirement>
-        <requirement type="package" version="2020.0">mkl</requirement>
-        <requirement type="package" version="*=mkl">blas</requirement>
+        <requirement type="package" version="2020.0">mkl</requirement><!-- this seems to be the last version of MKL which supports the "MKL_DEBUG_CPU_TYPE" environment variable -->
+        <requirement type="package" version="*=mkl">blas</requirement><!-- using MKL instead of other BLAS can significantly improve performance on some hardware, cf. https://stackoverflow.com/questions/62783262/why-is-numpy-with-ryzen-threadripper-so-much-slower-than-xeon -->
     </requirements>
     <command detect_errors="aggressive">
     <![CDATA[
@@ -68,7 +68,7 @@
     ]]>
     </command>
     <environment_variables>
-        <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable>
+        <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable><!-- this enables accelerated CPU instruction sets on AMD hardware, does nothing in Intel hardware, thus no need to change this -->
     </environment_variables>
     <inputs>
         <param name="dataset" type="data" format="tiff,png" label="Dataset" />