Setup v0.9.4

Setup dependencies, docker, version numbers, spack.

See merge request !200

Release 0.9.3


See merge request !199

Resolve "Shared file metadata congestion"

During write operations, the client must update the file size on the responsible metadata daemon. The write size cache
can reduce the metadata load on the daemon and reduce the number of RPCs during write operations, especially for many
small I/O operations. In the past, we have observed that a daemon can become network-congested, especially for single shared files, many processes, and small I/O operations, which bottlenecks the overall I/O throughput. Nevertheless, the cache can have a broad impact on small I/O operations as 1 RPC for updating the size is removed which already improves small file I/O on a single node.

Note that this cache may impact file size consistency in which stat operations may not reflect the actual file size
until the file is closed. The cache does not impact the consistency of the file data itself. We did not observe any issues with the cache for HPC applications and benchmarks, but it technically breaks POSIX. So, for now, I suggest it to be experimental and opt-in.

- `LIBGKFS_WRITE_SIZE_CACHE` - Enable caching the write size of files (default: OFF).
- `LIBGKFS_WRITE_SIZE_CACHE_THRESHOLD` - Set the number of write operations after which the file size is synchronized
  with the corresponding daemon (default: 1000). The file size is further synchronized when the file is `close()`d or
  when `fsync()` is called.

Depends on !194

Closes #62

Closes #62

See merge request !193

, enable by config and disable via `LIBGKFS_WRITE_SIZE_CACHE=OFF`. Flush happens on close/fsync. flush threshold can be changed via config or `LIBGKFS_WRITE_SIZE_CACHE_THRESHOLD=100` 

Resolve "Tests fail when symlink support is disabled"

This MR does several things:
1. `SUPPORT_SYMLINKS` is now disabled by default. It didn't do much in the first place and only affects incomplete code. The corresponding README entry has been removed. The only thing it does support is accessing GekkoFS from a foreign namespace via a symbolic link. However, only `stat` seems to be working.
2. `GKFS_FOLLOW_EXTERNAL_SYMLINKS` was also disabled by default in this [MR](!183). This caused the `test_symlink` to fail as it tested external symlinks into GekkoFS, not actual symlinks within GekkoFS. This can only be done via `lstat()` for each component of the path which is a performance risk under certain circumstances. Overall, this is the relevant CMake variable for the test.
3. Unify code formatting for CMake files.

Closes #298

Closes #298

See merge request !198

Resolve "Tests failing due to marshmallow"

Closes #297

Closes #297

See merge request !197

Resolve "Add dentry cache"

This MR adds a directory entry cache for the client to avoid a huge number of stat calls after readdir, e.g., for `ls -l` type operations. It is experimental and thus disabled by default. Can be enabled via `include/config.hpp` or with the env variable `LIBGKFS_DENTRY_CACHE=ON/OFF`.

It works by using the `extended_dir_entry` RPC to receive some metadata along the the dentries from the daemons. This metadata is then placed into the cache and retrieved in a stat operation (for a cache miss, an RPC is sent with vanilla functionality). The cache is discarded upon close but can be changed via `include/config.hpp`. Note, this may cause semantical issues (removed files will remain in the cache forever).

The performance improvements are already noticeable locally for a couple 1000 files.

Depends on !195

Closes #292

Closes #292

See merge request !194

Env variable overrides config.hpp

This uses the extended dir RPC call.

Resolve "Refactor path resolution"

Refactors path resolve mechanism and adds two new CMake options:

- `GKFS_USE_LEGACY_PATH_RESOLVE` - Use the legacy implementation of the resolve function, deprecated (default: OFF)
- `GKFS_FOLLOW_EXTERNAL_SYMLINKS` - Enable support for following external links for resolving the path (default: OFF)
    - This is automatically enabled in the deprecated version and causes an `lstat()` system call on each individual path component. This has been an issue in the past where performance was considerably impacted by the mountpath being placed within the parallel file system. 
    - It is now disabled by default to improve performance. In case, it causes issues, we can re-enable it.


Closes #281

Closes #281

See merge request !183

Resolve "File system expansion during runtime"

# Description

GekkoFS supports extending the current daemon configuration to additional compute nodes. This includes redistribution
of the existing data and metadata and therefore scales file system performance and capacity of existing data. Note,
that it is the user's responsibility to not access the GekkoFS file system during redistribution. A corresponding feature
that is transparent to the user is planned. Note also, if the GekkoFS proxy is used, they need to be manually restarted, after expansion.

To enable this feature, the following CMake compilation flags are required to build the `gkfs_malleability` tool: `-DGKFS_BUILD_TOOLS=ON`.
The `gkfs_malleability` tool is then available in the `build/tools` directory. Please consult `-h` for its arguments.
While the tool can be used manually to expand the file system, the `scripts/run/gkfs` script should be used instead which invokes the `gkfs_malleability` tool.

The only requirement for extending the file system is a hostfile containing the hostnames/IPs of the new nodes (one line per host).
Example starting the file system. The `DAEMON_NODELIST` in the `gkfs.conf` is set to a hostfile containing the initial set of file system nodes.:
```bash
~/gekkofs/scripts/run/gkfs -c ~/run/gkfs_verbs_expandtest.conf start
* [gkfs] Starting GekkoFS daemons (4 nodes) ...
* [gkfs] GekkoFS daemons running
* [gkfs] Startup time: 10.853 seconds
```
... Some computation ...

Expanding the file system. Using `-e <hostfile>` to specify the new nodes. Redistribution is done automatically with a progress bar. 
When finished, the file system is ready to use in the new configuration:
```bash
~/gekkofs/scripts/run/gkfs -c ~/run/gkfs_verbs_expandtest.conf -e ~/hostfile_expand expand
* [gkfs] Starting GekkoFS daemons (8 nodes) ...
* [gkfs] GekkoFS daemons running
* [gkfs] Startup time: 1.058 seconds
Expansion process from 4 nodes to 12 nodes launched...
* [gkfs] Expansion progress:
[####################] 0/4 left
* [gkfs] Redistribution process done. Finalizing ...
* [gkfs] Expansion done.
```
Stop the file system:
```bash
~/gekkofs/scripts/run/gkfs -c ~/run/gkfs_verbs_expandtest.conf stop
* [gkfs] Stopping daemon with pid 16462
srun: sending Ctrl-C to StepId=282378.1
* [gkfs] Stopping daemon with pid 16761
srun: sending Ctrl-C to StepId=282378.2
* [gkfs] Shutdown time: 1.032 seconds
```

# Results
IOR results for writing/reading 768 GiB sequentially (192 procs) before and after expansion

![image](/uploads/57bd8f3a07a56c496b1ae0b096da24ef/image.png)

MDTest results for creating, stating, removing, 19200000 (192 procs) before and after expansion

![image](/uploads/7e2f58d864789e657140ced3e9e9716e/image.png)

Closes #294

Closes #294

See merge request !196

Proxy must be restarted to know about the file system extension.