data_integrity test remaining statx() to stat()

Closes #115

See merge request hpc/gekkofs!59

Resolve "[daemon] chunk storage backend crashes the server on error"

Closes #75

The `ChunkStorage` backend class on the daemon was throwing `system_errors` without being caught, crashing the server in the process. `ChunkStorage` now uses a designated error class for errors that might occur. In addition the dependency to Argobots was removed which was used to trigger `ABT_eventuals`, laying ground work for future non-Argobots IO implementations. Further, the whole class was refactored for consistency and failure resistance.

A new class `ChunkOperation` is introduced which wraps Argobots' IO task operations which allows the removal of IO queue specific code within RPC handlers, i.e., read and write handlers. The idea is to separate eventuals, tasks and their arguments from handler logic into a designated class. Therefore, an object of an inherited class of `ChunkOperation` is instantiated within the handlers that drives all IO tasks. The corresponding code was added to the read and write RPC handlers. Note, `ChunkOperation` is not thread-safe and is supposed to be called by a single thread.

In addition, truncate was reworked for error handling (it crashed the server on error) and that it uses the IO queue as well since truncate causes a write operation and should not overtake IO tasks in the queue.

The chunk stat rpc handler was refactored for error handling and to use error codes as well. 

Further minor changes:
- dead chunk stat code has been removed
- some namespaces were missing: `gkfs::rpc`
- more flexible handler cleanup and response code
- fixed a bug where the chunk dir wasn't removed when the metadata didn't exist on the same node

Misc:
There was some discussion about putting the removal of the chunk directory into the IO queue as well with the same argument as truncate, but I refrain to do so as it would likely notably increase remove performance. I think, we can put this under *eventual consistency* and call it a day for now. Truncate was another story as glibc makes heavy use of truncate in various operations.

See merge request hpc/gekkofs!32

Marc Vef authored Feb 25, 2020 and Alberto Miranda committed Jul 28, 2020

The `ChunkStorage` backend class on the daemon was throwing `system_errors` without being caught, crashing the server in the process. `ChunkStorage` now uses a designated error class for errors that might occur. In addition the dependency to Argobots was removed which was used to trigger `ABT_eventuals`, laying ground work for future non-Argobots IO implementations. Further, the whole class was refactored for consistency and failure resistance.

A new class `ChunkOperation` is introduced which wraps Argobots' IO task operations which allows the removal of IO queue specific code within RPC handlers, i.e., read and write handlers. The idea is to separate eventuals, tasks and their arguments from handler logic into a designated class. Therefore, an object of an inherited class of `ChunkOperation` is instantiated within the handlers that drives all IO tasks. The corresponding code was added to the read and write RPC handlers. Note, `ChunkOperation` is not thread-safe and is supposed to be called by a single thread.

In addition, truncate was reworked for error handling (it crashed the server on error) and that it uses the IO queue as well since truncate causes a write operation and should not overtake IO tasks in the queue.

The chunk stat rpc handler was refactored for error handling and to use error codes as well. 

Further minor changes:
- dead chunk stat code has been removed
- some namespaces were missing: `gkfs::rpc`
- more flexible handler cleanup and response code
- fixed a bug where the chunk dir wasn't removed when the metadata didn't exist on the same node

Resolve "Native Omni-Path support"

Closes #59

See merge request hpc/gekkofs!56

Minor dependency script updates:

* adding more optional versions to the dependency scripts: RocksDB and syscall_intercept with glibc3 fix as more systems are updated to >glibc3
* Cloning libfabric instead of downloading the tarball. This is because it is configured with a specific autotools version which is not available on all systems. Cloning allows generating `configure` dynamically.
* daemon metadata backend now links to Dynamic Loader which is required by newer systems (not sure when this happened) and newer rocksdb versions
* removing python startup scripts since they are no longer supported and are confusing if part of the git repo

See merge request hpc/gekkofs!57

Resolve "[Testing] test_data fails when statx is not available"

Closes #115

See merge request hpc/gekkofs!54

Resolve "missing fsync"

Closes #110

See merge request !52

Resolve "Add I/O tests"

Closes #107

See merge request hpc/gekkofs!47

Check for statx support

See merge request !49