📝 add hints on troubleshooting running jobs

seqera/setup_infrastructure.md

@@ -24,7 +24,6 @@ a Managed Identity and Batch Pool.
 
 - Admin permissions to add credentials, compute environment(s) and pipelines to a workspace 
 
-
 ## On VMs as nodes in a pool
 Nodes in a pool are described based on the VM naming convention:
 
@@ -35,3 +34,60 @@ See also [Azure Batch documentation](https://learn.microsoft.com/en-us/azure/bat
 > Local storage of a VM is one-to-one in line with the number of CPUs. See the `Local Storage` tab
 > for a machine in a series to find out more. See for example the
 > [Ddsv4 sizes series](https://learn.microsoft.com/en-us/azure/virtual-machines/sizes/general-purpose/ddsv4-series?tabs=sizestoragelocal).
+
+## Spreading vs Packing nodes in a pool
+
+Defines how jobs are packed on nodes. Packing puts as many tasks as possible on a single
+node. Spreading starts new nodes for each task by default. See the documentation for
+more details:
+[azure/batch/batch-parallel-node-tasks](https://learn.microsoft.com/en-us/azure/batch/batch-parallel-node-tasks)
+
+## Troubleshooting
+
+### Connection issues
+
+If you encounter connection issues when launching pipelines from Seqera using 
+Azure Batch compute environment, try to increase the timeout settings in the
+Compute Environment configuration on Seqera Platform to around 8-16 hours.
+
+```
+NXF_OPTS="-Dsun.net.client.defaultConnectTimeout=30000 -Dsun.net.client.defaultReadTimeout=60000"
+```
+
+Here are some example screenshots for setting it as global Environment variables
+
+![Timeout settings in Compute Environment](assets/seqera_compute_env_0.png)
+![Timeout settings in Compute Environment](assets/seqera_compute_env_1.png)
+
+So you will need to set the `NXF_OPTS` environment variable in the Compute Environment 
+configuration on Seqera Platform to
+
+```
+-Dsun.net.client.defaultConnectTimeout=30000 -Dsun.net.client.defaultReadTimeout=60000
+```
+
+<details>
+<summary>Example error message:</summary>
+
+```bash
+The workflow execution failed to start. Exit status: 1
+
+ERROR ~ Unable to access config file 'https://api.cloud.seqera.io/ephemeral/<ephemeral-id>' -- Cause: Server returned HTTP response code: 403 for URL: https://api.cloud.seqera.io/ephemeral/<ephemeral-id>
+
+  Server returned HTTP response code: 403 for URL: https://api.cloud.seqera.io/ephemeral/<ephemeral-id>
+
+
+ -- Check 'nf-2OSwVxmg7B2QQt.log' file for details
+```
+ </details>
+
+
+### VM sizes
+
+To handle workflows with a mix of low and high memory requirements, consider
+to let Seqera create multiple Azure Batch pools with different VM sizes based
+on process requirements. This can be achieved by using the `autopool` feature.
+
+- See [nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#auto-pools)
+- See [Seqera documentation](https://docs.seqera.io/platform-cloud/enterprise/advanced-topics/manual-azure-batch-setup#option-4-use-the-nextflow-autopool-feature)
+