Update Pulsar to 0.14.0, and move Stampede 2's back to a filesystem t…

…hat isn't forcibly cleaned.

env/common/host_vars/login2.stampede2.tacc.utexas.edu.yml

@@ -4,31 +4,33 @@
 #
 
 # FIXME:
+#   - conda installed by hand
+#   - __python@3.8 conda-forge env installed by hand
 #   - supervisor configured by hand
 #   - parrot installed by hand in ~xcgalaxy
 #   - CVMFS keys installed by hand in ~xcgalaxy
 #   - no stratum1 failover for parrot, not sure if it's possible
 #   - running a branch of pulsar with a hardcoded parrot wrapper
 
-#_stampede_work_root: "/work/galaxy/{{ galaxy_instance_codename }}"
+_stampede_work_root: "/work/03166/xcgalaxy/stampede2"
 _stampede_scratch_root: "/scratch/03166/xcgalaxy"
-_stampede_instance_root: "{{ _stampede_scratch_root }}/{{ galaxy_instance_codename }}"
+_stampede_instance_root: "{{ _stampede_work_root }}/{{ galaxy_instance_codename }}"
 _stampede_galaxy_root: "/cvmfs/{{ galaxy_cvmfs_repo }}/galaxy"
 
 # Isn't this what conda's special virtualenv is supposed to fix?
-host_links:
-  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libffi.so"
-    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libffi.so"
-  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libffi.so.7"
-    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libffi.so.7"
-  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libssl.so"
-    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libssl.so"
-  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libssl.so.1.1"
-    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libssl.so.1.1"
-  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libcrypto.so"
-    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libcrypto.so"
-  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libcrypto.so.1.1"
-    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libcrypto.so.1.1"
+#host_links:
+#  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libffi.so"
+#    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libffi.so"
+#  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libffi.so.7"
+#    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libffi.so.7"
+#  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libssl.so"
+#    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libssl.so"
+#  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libssl.so.1.1"
+#    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libssl.so.1.1"
+#  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libcrypto.so"
+#    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libcrypto.so"
+#  - src: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/lib/libcrypto.so.1.1"
+#    path: "{{ _stampede_instance_root }}/pulsar/venv/lib/libcrypto.so.1.1"
 
 host_directories:
   - path: "{{ pulsar_root }}/log"
@@ -41,13 +43,13 @@ pulsar_root: "{{ _stampede_instance_root }}/pulsar"
 #pulsar_dependencies_dir: "/cvmfs/{{ galaxy_cvmfs_repo }}/deps"
 _pulsar_dependencies_dir: "/cvmfs/{{ galaxy_cvmfs_repo }}/deps"
 pulsar_persistence_dir: "{{ pulsar_root }}/var/persisted_data"
-pulsar_staging_dir: "{{ _stampede_instance_root }}/staging"
+pulsar_staging_dir: "{{ _stampede_scratch_root }}/{{ galaxy_instance_codename }}/staging"
 
 galaxy_user: xcgalaxy
 pulsar_privsep_user: "{{ galaxy_user }}"
 # Override group_vars version
 pulsar_package_name: "git+https://github.com/natefoo/pulsar.git@stampede-parrot"
-pip_virtualenv_command: "{{ _stampede_scratch_root }}/conda/envs/_pulsar_/bin/virtualenv"
+pip_virtualenv_command: "{{ _stampede_work_root }}/conda/envs/__python@3.8/bin/python3 -m venv"
 pip_extra_args: "--index-url https://wheels.galaxyproject.org/ --extra-index-url https://pypi.org/simple"
 
 pulsar_drmaa_library_path: "{{ _stampede_instance_root }}/slurm-drmaa/lib/libdrmaa.so"

env/common/host_vars/vm027.bridges.psc.edu.yml

@@ -4,11 +4,20 @@
 #
 
 # FIXME:
+#   - conda installed by hand
+#   - __python@3.8 conda-forge env installed by hand
+#   - __curl@7.71 env installed by hand
 #   - supervisor configured by hand
 #   - parrot installed by hand in ~xcgalaxy
 #   - CVMFS keys installed by hand in ~xcgalaxy
 #   - running a branch of pulsar with a hardcoded parrot wrapper
 
+# default $PATH contains puppet bin/sbin, which contain a newer curl that isn't found at pycurl runtime
+pulsar_env:
+  PATH: /pylon5/mc48nsp/xcgalaxy/conda/envs/__curl@7.71/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/bin:/sbin:/home/xcgalaxy/.local/bin:/home/xcgalaxy/bin
+  # FIXME: isn't working, using LD_LIBRARY_PATH in supervisor for the moment
+  #LD_RUN_PATH: /pylon5/mc48nsp/xcgalaxy/conda/envs/__curl@7.71/lib
+
 _bridges_home_root: "/home/xcgalaxy/{{ galaxy_instance_codename }}"
 _bridges_scratch_root: "/pylon5/mc48nsp/xcgalaxy/{{ galaxy_instance_codename }}"
 _bridges_galaxy_root: "/cvmfs/{{ galaxy_cvmfs_repo }}/galaxy"
@@ -26,9 +35,12 @@ galaxy_user: xcgalaxy
 pulsar_privsep_user: "{{ galaxy_user }}"
 # Override group_vars version
 pulsar_package_name: "git+https://github.com/natefoo/pulsar.git@stampede-parrot"
-pip_virtualenv_command: "/home/xcgalaxy/virtualenv/bin/virtualenv"
+#pip_virtualenv_command: "/home/xcgalaxy/virtualenv/bin/virtualenv"
+pip_virtualenv_command: "/pylon5/mc48nsp/xcgalaxy/conda/envs/__python@3.8/bin/python3 -m venv"
 pip_extra_args: "--index-url https://wheels.galaxyproject.org/ --extra-index-url https://pypi.org/simple"
 
+pulsar_pycurl_ssl_library: openssl
+
 pulsar_drmaa_library_path: "{{ _bridges_home_root }}/slurm-drmaa/lib/libdrmaa.so"
 
 pulsar_dependency_resolvers:

env/common/pulsar.yml

@@ -1,6 +1,7 @@
 ---
 
 - hosts: pulsarservers
+  environment: "{{ pulsar_env | default({}) }}"
   roles:
     # set up pulsar
     - galaxyproject.pulsar

env/main/group_vars/pulsarservers/vars.yml

@@ -15,7 +15,7 @@ galaxy_instance_hostname: usegalaxy.org
 #pulsar_package_name: "git+https://github.com/galaxyproject/pulsar.git@ff2208baf43f6afb9770316e474d15f69c9fd4f9"
 #pulsar_package_name: "git+https://github.com/galaxyproject/pulsar.git@2bfc784301c12634b6026113473767f1e3f4d017"
 #pulsar_package_name: "git+https://github.com/natefoo/pulsar.git@stampede-parrot"
-pulsar_package_version: "0.13.0"
+pulsar_package_version: "0.14.0"
 pulsar_venv_dir: "{{ pulsar_root }}/venv"
 pulsar_config_dir: "{{ pulsar_root }}/config"
 pulsar_optional_dependencies:

env/test/group_vars/pulsarservers/vars.yml

@@ -12,7 +12,7 @@ galaxy_instance_hostname: test.galaxyproject.org
 
 ## used by: galaxyproject.pulsar
 #pulsar_package_name: "git+https://github.com/galaxyproject/pulsar.git@2bfc784301c12634b6026113473767f1e3f4d017"
-pulsar_package_version: "0.13.0"
+pulsar_package_version: "0.14.0"
 pulsar_venv_dir: "{{ pulsar_root }}/venv"
 pulsar_config_dir: "{{ pulsar_root }}/config"
 pulsar_optional_dependencies: