# 4. Frequently asked questions (FAQ)

- About the project

  - Where did the name Charliecloud come from?

  - How do you spell Charliecloud?

- Errors

  - How do I read the `ch-run` error messages?

  - Tarball build fails with “No command specified”

  - `ch-run` fails with “can’t re-mount image read-only”

- Unexpected behavior

  - What do the version numbers mean?

  - `--uid 0` lets me read files I can’t otherwise!

  - Why does `ping` not work?

  - Why is MATLAB trying and failing to change the group of `/dev/pts/0`?

  - `ch-builder2tar` gives incorrect image sizes

  - My second-level directory `dev` is empty

  - My password that contains digits doesn’t work in VirtualBox console

- How do I ...

  - My app needs to write to `/var/log`, `/run`, etc.

  - Which specific `sudo` commands are needed?

  - OpenMPI Charliecloud jobs don’t work

    - `mpirun` can’t launch jobs

    - Communication between ranks on the same node fails

    - I get a bunch of independent rank-0 processes when launching with `srun`

  - How do I run X11 apps?

  - How do I specify an image reference?

  - Can I build or pull images using a tool Charliecloud doesn’t know about?

## 4.1. About the project

### 4.1.1. Where did the name Charliecloud come from?

Charlie — Charles F. McMillan was director of Los Alamos National Laboratory from June 2011 until December 2017, i.e., at the time Charliecloud was started in early 2014. He is universally referred to as “Charlie” here.

cloud — Charliecloud provides cloud-like flexibility for HPC systems.

### 4.1.2. How do you spell Charliecloud?

We try to be consistent with Charliecloud — one word, no camel case. That is, Charlie Cloud and CharlieCloud are both incorrect.

## 4.2. Errors

### 4.2.1. How do I read the `ch-run` error messages?

`ch-run` error messages look like this:

    $ ch-run foo -- echo hello
    ch-run[25750]: can't find image: foo: No such file or directory (ch-run.c:107 2)

There is a lot of information here, and it comes in this order:

1. Name of the executable; always `ch-run`.

2. Process ID in square brackets; here `25750`. This is useful when debugging parallel `ch-run` invocations.

3. Colon.

4. Main error message; here `can't find image: foo`. This should be informative as to what went wrong, and if it’s not, please file an issue, because you may have found a usability bug. Note that in some cases you may encounter the default message `error`; if this happens and you’re not doing something very strange, that’s also a usability bug.

5. Colon (but note that the main error itself can contain colons too), if and only if the next item is present.

6. Operating system’s description of the the value of `errno`; here `No such file or directory`. Omitted if not applicable.

7. Open parenthesis.

8. Name of the source file where the error occurred; here `ch-run.c`. This and the following item tell developers exactly where `ch-run` became confused, which greatly improves our ability to provide help and/or debug.

9. Source line where the error occurred.

10. Value of `errno` (see C error codes in Linux for the full list of possibilities).

11. Close parenthesis.

Note: Despite the structured format, the error messages are not guaranteed to be machine-readable.

### 4.2.2. Tarball build fails with “No command specified”

The full error from `ch-builder2tar` or `ch-build2dir` is:

    docker: Error response from daemon: No command specified.

You will also see it with various plain Docker commands.

This happens when there is no default command specified in the Dockerfile or any of its ancestors. Some base images specify one (e.g., Debian) and others don’t (e.g., Alpine). Docker requires this even for commands that don’t seem like they should need it, such as `docker create` (which is what trips up Charliecloud).

The solution is to add a default command to your Dockerfile, such as `CMD ["true"]`.

### 4.2.3. `ch-run` fails with “can’t re-mount image read-only”

Normally, `ch-run` re-mounts the image directory read-only within the container. This fails if the image resides on certain filesystems, such as NFS (see issue #9). There are two solutions:

1. Unpack the image into a different filesystem, such as `tmpfs` or local disk. Consult your local admins for a recommendation. Note that Lustre is probably not a good idea because it can give poor performance for you and also everyone else on the system.

2. Use the `-w` switch to leave the image mounted read-write. This may have an impact on reproducibility (because the application can change the image between runs) and/or stability (if there are multiple application processes and one writes a file in the image that another is reading or writing).

## 4.3. Unexpected behavior

### 4.3.1. What do the version numbers mean?

Released versions of Charliecloud have a pretty standard version number, e.g. 0.9.7.

Work leading up to a released version also has version numbers, to satisfy tools that require them and to give the executables something useful to report on `--version`, but these can be quite messy. We refer to such versions informally as pre-releases, but Charliecloud does not have formal pre-releases such as alpha, beta, or release candidate.

Pre-release version numbers are not in order, because this work is in a DAG rather than linear, except they precede the version we are working towards. If you’re dealing with these versions, use Git.

Pre-release version numbers are the version we are working towards, followed by: `~pre`, the branch name if not `master` with non-alphanumerics removed, the commit hash, and finally `dirty` if the working directory had uncommitted changes.

Examples:

> - `0.2.0` : Version 0.2.0. Released versions don’t include Git information, even if built in a Git working directory.

> - `0.2.1~pre` : Some snapshot of work leading up to 0.2.1, built from source code where the Git information has been lost, e.g. the tarballs Github provides. This should make you wary because you don’t have any provenance. It might even be uncommitted work or an abandoned branch.

> - `0.2.1~pre+1a99f42` : Master branch commit 1a99f42, built from a clean working directory (i.e., no changes since that commit).

> - `0.2.1~pre+foo1.0729a78` : Commit 0729a78 on branch `foo-1`, `foo_1`, etc. built from clean working directory.

> - `0.2.1~pre+foo1.0729a78.dirty` : Commit 0729a78 on one of those branches, plus un-committed changes.

### 4.3.2. `--uid 0` lets me read files I can’t otherwise!

Some permission bits can give a surprising result with a container UID of 0. For example:

    $ whoami
    reidpr
    $ echo surprise > ~/cantreadme
    $ chmod 000 ~/cantreadme
    $ ls -l ~/cantreadme
    ---------- 1 reidpr reidpr 9 Oct  3 15:03 /home/reidpr/cantreadme
    $ cat ~/cantreadme
    cat: /home/reidpr/cantreadme: Permission denied
    $ ch-run /var/tmp/hello cat ~/cantreadme
    cat: /home/reidpr/cantreadme: Permission denied
    $ ch-run --uid 0 /var/tmp/hello cat ~/cantreadme
    surprise

At first glance, it seems that we’ve found an escalation – we were able to read a file inside a container that we could not read on the host! That seems bad.

However, what is really going on here is more prosaic but complicated:

1. After `unshare(CLONE_NEWUSER)`, `ch-run` gains all capabilities inside the namespace. (Outside, capabilities are unchanged.)

2. This include `CAP_DAC_OVERRIDE`, which enables a process to read/write/execute a file or directory mostly regardless of its permission bits. (This is why root isn’t limited by permissions.)

3. Within the container, `exec(2)` capability rules are followed. Normally, this basically means that all capabilities are dropped when `ch-run` replaces itself with the user command. However, if EUID is 0, which it is inside the namespace given `--uid 0`, then the subprocess keeps all its capabilities. (This makes sense: if root creates a new process, it stays root.)

4. `CAP_DAC_OVERRIDE` within a user namespace is honored for a file or directory only if its UID and GID are both mapped. In this case, `ch-run` maps `reidpr` to container `root` and group `reidpr` to itself.

5. Thus, files and directories owned by the host EUID and EGID (here `reidpr:reidpr`) are available for all access with `ch-run --uid 0`.

This is not an escalation. The quirk applies only to files owned by the invoking user, because `ch-run` is unprivileged outside the namespace, and thus he or she could simply `chmod` the file to read it. Access inside and outside the container remains equivalent.

References:

- http://man7.org/linux/man-pages/man7/capabilities.7.html

- http://lxr.free-electrons.com/source/kernel/capability.c?v=4.2#L442

- http://lxr.free-electrons.com/source/fs/namei.c?v=4.2#L328

### 4.3.3. Why does `ping` not work?

`ping` fails with “permission denied” or similar under Charliecloud, even if you’re UID 0 inside the container:

    $ ch-run $IMG -- ping 8.8.8.8
    PING 8.8.8.8 (8.8.8.8): 56 data bytes
    ping: permission denied (are you root?)
    $ ch-run --uid=0 $IMG -- ping 8.8.8.8
    PING 8.8.8.8 (8.8.8.8): 56 data bytes
    ping: permission denied (are you root?)

This is because `ping` needs a raw socket to construct the needed `ICMP ECHO` packets, which requires capability `CAP_NET_RAW` or root. Unprivileged users can normally use `ping` because it’s a setuid or setcap binary: it raises privilege using the filesystem bits on the executable to obtain a raw socket.

Under Charliecloud, there are multiple reasons `ping` can’t get a raw socket. First, images are unpacked without privilege, meaning that setuid and setcap bits are lost. But even if you do get privilege in the container (e.g., with `--uid=0`), this only applies in the container. Charliecloud uses the host’s network namespace, where your unprivileged host identity applies and `ping` still can’t get a raw socket.

The recommended alternative is to simply try the thing you want to do, without testing connectivity using `ping` first.

### 4.3.4. Why is MATLAB trying and failing to change the group of `/dev/pts/0`?

MATLAB and some other programs want pseudo-TTY (PTY) files to be group-owned by `tty`. If it’s not, Matlab will attempt to `chown(2)` the file, which fails inside a container.

The scenario in more detail is this. Assume you’re user `charlie` (UID=1000), your primary group is `nerds` (GID=1001), `/dev/pts/0` is the PTY file in question, and its ownership is `charlie:tty` (`1000:5`), as it should be. What happens in the container by default is:

1. MATLAB `stat(2)`s `/dev/pts/0` and checks the GID.

2. This GID is `nogroup` (65534) because `tty` (5) is not mapped on the host side (and cannot be, because only one’s EGID can be mapped in an unprivileged user namespace).

3. MATLAB concludes this is bad.

4. MATLAB executes `chown("/dev/pts/0", 1000, 5)`.

5. This fails because GID 5 is not mapped on the guest side.

6. MATLAB pukes.

The workaround is to map your EGID of 1001 to 5 inside the container (instead of the default 1001:1001), i.e. `--gid=5`. Then, step 4 succeeds because the call is mapped to `chown("/dev/pts/0", 1000, 1001)` and MATLAB is happy.

### 4.3.5. `ch-builder2tar` gives incorrect image sizes

`ch-builder2tar` often finishes before the progress bar is complete. For example:

    $ ch-builder2tar mpihello /var/tmp
     373MiB 0:00:21 [============================>                 ] 65%
    146M /var/tmp/mpihello.tar.gz

In this case, the `.tar.gz` contains 392 MB uncompressed:

    $ zcat /var/tmp/mpihello.tar.gz | wc
    2740966 14631550 392145408

But Docker thinks the image is 597 MB:

    $ sudo docker image inspect mpihello | fgrep -i size
            "Size": 596952928,
            "VirtualSize": 596952928,

We’ve also seen cases where the Docker-reported size is an underestimate:

    $ ch-builder2tar spack /var/tmp
     423MiB 0:00:22 [============================================>] 102%
    162M /var/tmp/spack.tar.gz
    $ zcat /var/tmp/spack.tar.gz | wc
    4181186 20317858 444212736
    $ sudo docker image inspect spack | fgrep -i size
            "Size": 433812403,
            "VirtualSize": 433812403,

We think that this is because Docker is computing size based on the size of the layers rather than the unpacked image. We do not currently have a fix; see issue #165.

### 4.3.6. My second-level directory `dev` is empty

Some image tarballs, such as official Ubuntu Docker images, put device files in `/dev`. These files prevent unpacking the tarball, because unprivileged users cannot create device files. Further, these files are not needed because `ch-run` overmounts `/dev` anyway.

We cannot reliably prevent device files from being included in the tar, because often that is outside our control, e.g. `docker export` produces a tarball. Thus, we must exclude them at unpacking time.

An additional complication is that `ch-tar2dir` can handle tarballs both with a single top-level directory and without, i.e. “tarbombs”. For example, best practice use of `tar` on the command line produces the former, while `docker export` (perhaps via `ch-builder2tar`) produces a tarbomb.

Thus, `ch-tar2dir` uses `tar --exclude` to exclude from unpacking everything under `./dev` and `*/dev`, i.e., directory `dev` appearing at either the first or second level are forced to be empty.

This yields false positives if you have a tarbomb image with a directory `dev` at the second level containing stuff you care about. Hopefully this is rare, but please let us know if it is your use case.

### 4.3.7. My password that contains digits doesn’t work in VirtualBox console

VirtualBox has confusing Num Lock behavior. Thus, you may be typing arrows, page up/down, etc. instead of digits, without noticing because console password fields give no feedback, not even whether a character has been typed.

Try using the number row instead, toggling Num Lock key, or SSHing into the virtual machine.

## 4.4. How do I ...

### 4.4.1. My app needs to write to `/var/log`, `/run`, etc.

Because the image is mounted read-only by default, log files, caches, and other stuff cannot be written anywhere in the image. You have three options:

1. Configure the application to use a different directory. `/tmp` is often a good choice, because it’s shared with the host and fast.

2. Use `RUN` commands in your Dockerfile to create symlinks that point somewhere writeable, e.g. `/tmp`, or `/mnt/0` with `ch-run --bind`.

3. Run the image read-write with `ch-run -w`. Be careful that multiple containers do not try to write to the same files.

### 4.4.2. Which specific `sudo` commands are needed?

For running images, `sudo` is not needed at all.

For building images, it depends on what you would like to support. For example, do you want to let users build images with Docker? Do you want to let them run the build tests?

We do not maintain specific lists, but you can search the source code and documentation for uses of `sudo` and `$DOCKER` and evaluate them on a case-by-case basis. (The latter includes `sudo` if needed to invoke `docker` in your environment.) For example:

    $ find . \(   -type f -executable \
               -o -name Makefile \
               -o -name '*.bats' \
               -o -name '*.rst' \
               -o -name '*.sh' \) \
             -exec egrep -H '(sudo|\$DOCKER)' {} \;

### 4.4.3. OpenMPI Charliecloud jobs don’t work

MPI can be finicky. This section documents some of the problems we’ve seen.

#### 4.4.3.1. `mpirun` can’t launch jobs

For example, you might see:

    $ mpirun -np 1 ch-run /var/tmp/mpihello -- /hello/hello
    App launch reported: 2 (out of 2) daemons - 0 (out of 1) procs
    [cn001:27101] PMIX ERROR: BAD-PARAM in file src/dstore/pmix_esh.c at line 996

We’re not yet sure why this happens — it may be a mismatch between the OpenMPI builds inside and outside the container — but in our experience launching with `srun` often works when `mpirun` doesn’t, so try that.

#### 4.4.3.2. Communication between ranks on the same node fails

OpenMPI has many ways to transfer messages between ranks. If the ranks are on the same node, it is faster to do these transfers using shared memory rather than involving the network stack. There are two ways to use shared memory.

The first and older method is to use POSIX or SysV shared memory segments. This approach uses two copies: one from Rank A to shared memory, and a second from shared memory to Rank B. For example, the `sm` byte transport layer (BTL) does this.

The second and newer method is to use the `process_vm_readv(2)` and/or `process_vm_writev(2)`) system calls to transfer messages directly from Rank A’s virtual memory to Rank B’s. This approach is known as cross-memory attach (CMA). It gives significant performance improvements in benchmarks, though of course the real-world impact depends on the application. For example, the `vader` BTL (enabled by default in OpenMPI 2.0) and `psm2` matching transport layer (MTL) do this.

The problem in Charliecloud is that the second approach does not work by default.

We can demonstrate the problem with LAMMPS molecular dynamics application:

    $ srun --cpus-per-task 1 ch-run /var/tmp/lammps_mpi -- \
      lmp_mpi -log none -in /lammps/examples/melt/in.melt
    [cn002:21512] Read -1, expected 6144, errno = 1
    [cn001:23947] Read -1, expected 6144, errno = 1
    [cn002:21517] Read -1, expected 9792, errno = 1
    [... repeat thousands of times ...]

With `strace(1)`, one can isolate the problem to the system call noted above:

    process_vm_readv(...) = -1 EPERM (Operation not permitted)
    write(33, "[cn001:27673] Read -1, expected 6"..., 48) = 48

The man page reveals that these system calls require that the process have permission to `ptrace(2)` one another, but sibling user namespaces do not. (You can `ptrace(2)` into a child namespace, which is why `gdb` doesn’t require anything special in Charliecloud.)

This problem is not specific to containers; for example, many settings of kernels with YAMA enabled will similarly disallow this access.

So what can you do? There are a few options:

- We recommend simply using the `--join` family of arguments to `ch-run`. This puts a group of `ch-run` peers in the same namespaces; then, the system calls work. See the ch-run man page for details.

- You can also sometimes turn off single-copy. For example, for `vader`, set the MCA variable `btl_vader_single_copy_mechanism` to `none`, e.g. with an environment variable:

      $ export OMPI_MCA_btl_vader_single_copy_mechanism=none

  `psm2` does not let you turn off CMA, but it does fall back to two-copy if CMA doesn’t work. However, this fallback crashed when we tried it.

- The kernel module XPMEM enables a different single-copy approach. We have not yet tried this, and the module needs to be evaluated for user namespace safety, but it’s quite a bit faster than CMA on benchmarks.

#### 4.4.3.3. I get a bunch of independent rank-0 processes when launching with `srun`

For example, you might be seeing this:

    $ srun ch-run /var/tmp/mpihello -- /hello/hello
    0: init ok cn036.localdomain, 1 ranks, userns 4026554634
    0: send/receive ok
    0: finalize ok
    0: init ok cn035.localdomain, 1 ranks, userns 4026554634
    0: send/receive ok
    0: finalize ok

We were expecting a two-rank MPI job, but instead we got two independent one-rank jobs that did not coordinate.

MPI ranks start as normal, independent processes that must find one another somehow in order to sync up and begin the coupled parallel program; this happens in `MPI_Init()`.

There are lots of ways to do this coordination. Because we are launching with the host’s Slurm, we need it to provide something for the containerized processes for such coordination. OpenMPI must be compiled to use what that Slurm has to offer, and Slurm must be told to offer it. What works for us is a something called “PMI2”. You can see if your Slurm supports it with:

    $ srun --mpi=list
    srun: MPI types are...
    srun: mpi/pmi2
    srun: mpi/openmpi
    srun: mpi/mpich1_shmem
    srun: mpi/mpich1_p4
    srun: mpi/lam
    srun: mpi/none
    srun: mpi/mvapich
    srun: mpi/mpichmx
    srun: mpi/mpichgm

If `pmi2` is not in the list, you must ask your admins to enable Slurm’s PMI2 support. If it is in the list, but you’re seeing this problem, that means it is not the default, and you need to tell Slurm you want it. Try:

    $ export SLURM_MPI_TYPE=pmi2
    $ srun ch-run /var/tmp/mpihello -- /hello/hello
    0: init ok wc035.localdomain, 2 ranks, userns 4026554634
    1: init ok wc036.localdomain, 2 ranks, userns 4026554634
    0: send/receive ok
    0: finalize ok

### 4.4.4. How do I run X11 apps?

X11 applications should “just work”. For example, try this Dockerfile:

    FROM debian:stretch
    RUN    apt-get update \
        && apt-get install -y xterm

Build it and unpack it to `/var/tmp`. Then:

    $ ch-run /scratch/ch/xterm -- xterm

should pop an xterm.

If your X11 application doesn’t work, please file an issue so we can figure out why.

### 4.4.5. How do I specify an image reference?

You must specify an image for many use cases, including `FROM` instructions, the source of an image pull (e.g. `ch-image pull` or `docker pull`), the destination of an image push, and adding image tags. Charliecloud calls this an image reference, but there appears to be no established name for this concept.

The syntax of an image reference is not well documented. This FAQ represents our understanding, which is cobbled together from the Dockerfile reference, the `docker tag` documentation, and various forum posts. It is not a precise match for how Docker implements it, but it should be close enough.

We’ll start with two complete examples with all the bells and whistles:

1. `example.com:8080/foo/bar/hello-world:version1.0`

2. `example.com:8080/foo/bar/hello-world@sha256:f6c68e2ad82a`

These references parse into the following components, in this order:

1. A valid hostname; we assume this matches the regular expression `[A-Za-z0-9.-]+`, which is very approximate. Optional; here `example.com`.

2. A colon followed by a decimal port number. If hostname is given, optional; otherwise disallowed; here `8080`.

3. If hostname given, a slash.

4. A path, with one or more components separated by slash. Components match the regex `[a-z0-9_.-]+`. Optional; here `foo/bar`. Pedantic details:

   - Under the hood, the default path is `library`, but this is generally not exposed to users.

   - Three or more underscores in a row is disallowed by Docker, but we don’t check this.

5. If path given, a slash.

6. The image name, which matches `[a-z0-9_.-]+`. Required; here `hello-world`.

7. Zero or one of:

   - A tag matching the regular expression `[A-Za-z0-9_.-]+` and preceded by a colon. Here `version1.0` (example 1).

   - A hexadecimal hash preceded by the string `@sha256:`. Here `f6c68e2ad82a` (example 2).

     - Note: Digest algorithms other than SHA-256 are in principle allowed, but we have not yet seen any.

Detail-oriented readers may have noticed the following gotchas:

- A hostname without port number is ambiguous with the leading component of a path. For example, in the reference `foo/bar/baz`, it is ambiguous whether `foo` is a hostname or the first (and only) component of the path `foo/bar`. The resolution rule is: if the ambiguous substring contains a dot, assume it’s a hostname; otherwise, assume it’s a path component.

- The only character than cannot go in a POSIX filename is slash. Thus, Charliecloud uses image references in filenames, replacing slash with percent (`%`). Because this character cannot appear in image references, the transformation is reversible.

  An alternate approach would be to replicate the reference path in the filesystem, i.e., path components in the reference would correspond directly to a filesystem path. This would yield a clearer filesystem structure. However, we elected not to do it because it complicates the code to save and clean up image reference-related data, and it does not address a few related questions, e.g. should the host and port also be a directory level.

Usually, most of the components are omitted. For example, you’ll more commonly see image references like:

> - `debian`, which refers to the tag `latest` of image `debian` from Docker Hub.

> - `debian:stretch`, which is the same except for tag `stretch`.

> - `fedora/httpd`, which is tag `latest` of `fedora/httpd` from Docker Hub.

See `charliecloud.py` for a specific grammar that implements this.

### 4.4.6. Can I build or pull images using a tool Charliecloud doesn’t know about?

Yes. Charliecloud deals in well-known UNIX formats like directories, tarballs, and SquashFS images. So, once you get your image into some format Charliecloud likes, you can enter the workflow.

For example, skopeo is a tool to pull images to OCI format, and umoci can flatten an OCI image to a directory. Thus, you can use the following commands to run an Alpine 3.9 image pulled from Docker hub:

    $ skopeo copy docker://alpine:3.9 oci:/tmp/oci:img
    [...]
    $ ls /tmp/oci
    blobs  index.json  oci-layout
    $ umoci unpack --rootless --image /tmp/oci:img /tmp/alpine:3.9
    [...]
    $ ls /tmp/alpine:3.9
    config.json
    rootfs
    sha256_2ca27acab3a0f4057852d9a8b775791ad8ff62fbedfc99529754549d33965941.mtree
    umoci.json
    $ ls /tmp/alpine:3.9/rootfs
    bin  etc   lib    mnt  proc  run   srv  tmp  var
    dev  home  media  opt  root  sbin  sys  usr
    $ ch-run /tmp/alpine:3.9/rootfs -- cat /etc/alpine-release
    3.9.5