Phylo patch

Dockerfile

@@ -2,6 +2,9 @@ FROM continuumio/anaconda3
 LABEL "author"="Mathieu Fourment"
 LABEL "company"="University of Technology Sydney"
 
+# bust cache and re-run all
+ADD http://date.jsontest.com /etc/builddate
+
 RUN apt-get update && \
 	apt-get install -y --no-install-recommends \
 		autoconf \
@@ -62,14 +65,17 @@ RUN ln -s /bitorch/benchmarks/benchmark.py /usr/local/bin/bitorch-benchmark \
 RUN . /opt/conda/etc/profile.d/conda.sh && conda activate bito && /usr/local/bin/bitorch-benchmark --help
 
 RUN git clone --depth 1 https://github.com/4ment/phylojax /phylojax
-RUN cd /phylojax && /opt/conda/envs/bito/bin/pip install jax==0.2.24 jaxlib . && /opt/conda/envs/bito/bin/phylojax --help
+RUN cd /phylojax && /opt/conda/envs/bito/bin/pip install jax==0.2.24 jaxlib==0.3.7 numpy==1.22 . && /opt/conda/envs/bito/bin/phylojax --help
 RUN ln -s /phylojax/benchmarks/benchmark.py /usr/local/bin/phylojax-benchmark \
     && chmod +x /usr/local/bin/phylojax-benchmark
 
 RUN pip install phylostan==1.0.5 && phylostan --help
+RUN pip install tqdm
 
-RUN git clone --depth 1 https://github.com/christiaanjs/treeflow.git /treeflow
-RUN cd /treeflow && /opt/conda/envs/bito/bin/pip install . 
+# workaround to bust cache if the master branch has been updated ... 
+# ADD https://api.github.com/repos/christiaanjs/treeflow/git/refs/heads/master /.git-hashref
+RUN git clone --depth 10 https://github.com/christiaanjs/treeflow.git /treeflow
+RUN cd /treeflow && git checkout e3414dcc9e764d06abc3e19c1d0f55110499e2ea && /opt/conda/envs/bito/bin/pip install . 
 RUN . /opt/conda/etc/profile.d/conda.sh && conda activate bito && treeflow_benchmark --help
 
 RUN echo "source activate bito" > ~/.bashrc

configs/rhino.config

@@ -7,26 +7,42 @@ manifest {
 }
 
 profiles {
+
+    standard {
+
+        process {
+            executor = 'local'
+            container = 'quay.io/matsengrp/autodiff-experiments:phylo_patch'
+            cpus = 4
+            memory = 20.GB
+        }
+
+        singularity {
+            enabled = true
+            autoMounts = true
+            cacheDir = '/fh/scratch/delete30/matsen_e/mathieu/temp/containers/'
+            runOptions = '--contain -W /tmp/'
+        }
+    }
+
+
     rhino {
         process {
             executor = 'slurm'
-            scratch = '/fh/scratch/delete30/matsen_e/mathieu/temp/nf-scratch/'
+            //scratch = '/fh/scratch/delete30/matsen_e/mathieu/temp/nf-scratch/'
             queue = 'campus-new'
-            cpus = 3
-            memory = 20.GB
-            //container = 'quay.io/matsengrp/autodiff-experiments:rhino_config'
-            container = '4ment/autodiff-experiments'
+            cpus = 4
+            memory = 32.GB
+            container = 'quay.io/matsengrp/autodiff-experiments:phylo_patch'
             time = '200h'
 
             withLabel: normal {
                 time = '5h'
             }
             withLabel: fast {
-                cpus=2
                 time = '60m'
             }
             withLabel: ultrafast{
-                cpus=2
                 time = '5m'
             }
         }

modules/macro_flu.nf

@@ -139,7 +139,7 @@ process PREPARE_TORCHTREE {
 }
 
 process RUN_TORCHTREE {
-  label 'fast'
+  label 'normal'
   label 'bito'
 
   errorStrategy 'ignore'
@@ -158,15 +158,16 @@ process RUN_TORCHTREE {
 
 process RUN_PHYLOJAX {
   label 'bito'
-
   errorStrategy 'ignore'
-
   publishDir "$params.results/macro/phylojax", mode: 'copy'
 
   input:
     tuple val(size), val(rep), path(tree_file), val(rate), path(seq_file)
   output:
     tuple path("phylojax.${size}.${rep}.txt"), path("phylojax.${size}.${rep}.log")
+
+  when:
+    size <= 750
   """
   { time \
   phylojax -i ${seq_file} \
@@ -181,19 +182,21 @@ process RUN_PHYLOJAX {
 }
 
 process RUN_TREEFLOW {
-  label 'fast'
   label 'bito'
 
+  errorStrategy 'ignore'
+
   publishDir "$params.results/macro/treeflow", mode: 'copy'
 
   input:
-    tuple val(size), val(rep), path(tree_file), path(seq_file)
+    tuple val(size), val(rep), path(tree_file), val(rate), path(seq_file)
   output:
     tuple path("treeflow.${size}.${rep}.txt"), path("treeflow.${size}.${rep}.log")
   """
   { time \
   treeflow_vi -i ${seq_file} \
               -t ${tree_file} \
+              --init-values clock_rate=${rate} \
               -n ${params.iterations} > treeflow.${size}.${rep}.txt ; } 2> treeflow.${size}.${rep}.log
   """
 }
@@ -222,7 +225,7 @@ workflow macro_flu {
 
   RUN_TORCHTREE(data_run.join(PREPARE_TORCHTREE.out, by: [0, 1]))
 
-  RUN_TREEFLOW(data_run)
+  RUN_TREEFLOW(data.map {it.take(5)} )
 
   ch_files = Channel.empty()
   ch_files = ch_files.mix(

modules/micro.nf

@@ -29,7 +29,7 @@ process RUN_PHYSHER_BENCHMARK {
 }
 
 process RUN_TORCHTREE_BENCHMARK {
-  label 'normal'
+  //label 'normal'
   label 'bito'
 
   publishDir "$params.results/micro/${phylox}", mode: 'copy'
@@ -67,6 +67,7 @@ process RUN_PHYLOJAX_BENCHMARK {
   tuple val(size), val(rep), path(lsd_newick), path(seq_file)
   output:
   path("phylojax.${size}.${rep}.csv")
+
   """
   phylojax-benchmark -i $seq_file \
                      -t $lsd_newick \
@@ -119,6 +120,9 @@ process COMBIME_CSV {
   tail -q -n+2 *[0-9].csv >> micro.csv
   """
 }
+//head -n1 ${files[0]} > micro
+//tail -q -n+2 *.csv >> micro
+//mv micro micro.csv
 
 workflow micro {
   take:

modules/treetime_validation.nf

@@ -4,6 +4,8 @@ nextflow.enable.dsl = 2
 
 params.subtrees = Channel.of(20, 50, 100, 200, 500, 750, 1000, 1250, 1500, 2000)
 params.subtrees_replicates = Channel.of(0..9)
+//params.subtrees = Channel.of(20, 50)//, 100, 200, 500, 750, 1000, 1250, 1500, 2000)
+//params.subtrees_replicates = Channel.of(0..1)
 params.base = "$baseDir"
 
 alignment_file = "$params.base/resources/flu_H3N2/H3N2_HA_2011_2013.fasta"

run_rhino.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 set -e
-source /app/lmod/lmod/init/profile
+# source /app/lmod/lmod/init/profile
 
 module load nextflow
 module load Singularity
@@ -10,9 +10,8 @@ export PATH=$SINGULARITYROOT/bin/:$PATH
 /usr/bin/time nextflow  \
     -C ./configs/rhino.config \
     run main.nf \
-    --results "$(date -I)-rhino-results" \
+    --results "batch-results-$(date -I)" \
     -profile rhino \
-    -with-report ./r_output/nextflow_report.html \
-    -work-dir ./r_output/work/ \
-    -with-trace \
-    -resume
+    -with-report "batch-results-$(date -I)"/nextflow_report.html \
+    -with-trace  "batch-results-$(date -I)"/trace.txt \
+    -work-dir "batch-results-$(date -I)/work/"

scripts/parse-trace.py

@@ -13,8 +13,12 @@
 with open(sys.argv[2], "r") as fp:
     for line in fp:
         a = line.split("\t")
+        if 'FAILED' in a or 'ABORTED' in a:
+            continue
         if "task_id" == a[0]:
             print("program\tsize\treplicate\t" + line, end="")
+        if a[1] not in dic:
+            continue
         elif "macro_flu:RUN_" in a[3]:
             for f in dic[a[1]]:
                 if ".txt" in f: