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‎docs/udocker/udocker-01.md‎

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@@ -419,67 +419,66 @@ The created container can be run as many times as you wish.
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## `udocker`: Execution engines I
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* Like in other container tools execution is achieved by providing `chroot` like functionality.
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* `udocker` supports several techniques to achieve the equivalent to a chroot without using privileges.
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* `udocker` supports several techniques to achieve the equivalent to a `chroot` without using privileges.
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* These techniques can be selected per container via execution modes implemented by execution engines.
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---
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## `udocker`: Execution engines II
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| Mode | Base | Description |
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| :---: | :---------: | :---------: |
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| P1 | PRoot | PTRACE accelerated (with SECCOMP filtering): *DEFAULT* |
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| P2 | PRoot | PTRACE non-accelerated (without SECCOMP filtering) |
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| R1 | runC | rootless unprivileged using user namespaces |
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| R2 | runC | rootless unprivileged using user namespaces + P1 |
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| R3 | runC | rootless unprivileged using user namespaces + P2 |
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| F1 | Fakechroot | with loader as argument and LD_LIBRARY_PATH |
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| Mode | Base | Description |
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| :---: | :---------: | :----------------------------------------------------------: |
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| P1 | PRoot | PTRACE accelerated (with SECCOMP filtering): *DEFAULT* |
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| P2 | PRoot | PTRACE non-accelerated (without SECCOMP filtering) |
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| R1 | runC | rootless unprivileged using user namespaces |
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| R2 | runC | rootless unprivileged using user namespaces + P1 |
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| R3 | runC | rootless unprivileged using user namespaces + P2 |
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| F1 | Fakechroot | with loader as argument and LD_LIBRARY_PATH |
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| F2 | Fakechroot | with modified loader, loader as argument and LD_LIBRARY_PATH |
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| F3 | Fakechroot | modified loader and ELF headers of binaries + libs changed |
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| F4 | Fakechroot | modified loader and ELF headers dynamically changed |
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| S1 | Singularity | where locally installed using chroot or user namespaces |
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| F3 | Fakechroot | modified loader and ELF headers of binaries + libs changed |
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| F4 | Fakechroot | modified loader and ELF headers dynamically changed |
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| S1 | Singularity | where locally installed using chroot or user namespaces |
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---
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## Selection in terms of performance
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| Mode | Base | Description |
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| :---: | :---------: | :---------: |
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| P1 | PRoot | System call intensive applications may suffer degradation |
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| P2 | PRoot | Same limitations as P1 apply. All system calls are traced causing higher overheads than P1 |
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| R1 | runC | Same performance as namespace based applications |
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| R2 | runC | Only for software installation and similar. Same performance as P1 |
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| R3 | runC | Only for software installation and similar. Same performance as P2 |
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| Mode | Base | Description |
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| :---: | :---------: | :---------------------------------------------------------------------------------------------: |
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| P1 | PRoot | System call intensive applications may suffer degradation |
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| P2 | PRoot | Same limitations as P1 apply. All system calls are traced causing higher overheads than P1 |
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| R1 | runC | Same performance as namespace based applications |
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| R2 | runC | Only for software installation and similar. Same performance as P1 |
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| R3 | runC | Only for software installation and similar. Same performance as P2 |
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| F1 | Fakechroot | All Fn modes have similar performance during execution. Frequently the Fn modes are the fastest |
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| F2 | Fakechroot | Same as F1 |
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| F3 | Fakechroot | Same as F1. Setup can be very slow |
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| F4 | Fakechroot | Same as F1. Setup can be very slow |
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| S1 | Singularity | Similar to Rn |
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| F2 | Fakechroot | Same as F1 |
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| F3 | Fakechroot | Same as F1. Setup can be very slow |
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| F4 | Fakechroot | Same as F1. Setup can be very slow |
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| S1 | Singularity | Similar to Rn |
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---
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## Selection in terms of interoperability I
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| Mode | Base | Description |
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| :---: | :---------: | :---------: |
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| P1 | PRoot | PTRACE + SECCOMP requires kernel >= 3.5. Can fall back to P2 if SECCOMP is unavailable |
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| Mode | Base | Description |
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| :---: | :---------: | :-----------------------------------------------------------------------------------------------------------------------: |
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| P1 | PRoot | PTRACE + SECCOMP requires kernel >= 3.5. Can fall back to P2 if SECCOMP is unavailable |
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| P2 | PRoot | Runs across a wide range of kernels even old ones. Can run with kernels and libraries that would fail with kernel too old |
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| R1 | runC | User namespace limitations apply |
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| R2 | runC | User namespace limitations apply. Same limitations as P1 also apply, this is a nested mode P1 over R |
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| R3 | runC | User namespace limitations apply. Same limitations as P2 also apply, this is a nested mode P2 over R |
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| R1 | runC | User namespace limitations apply |
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| R2 | runC | User namespace limitations apply. Same limitations as P1 also apply, this is a nested mode P1 over R |
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| R3 | runC | User namespace limitations apply. Same limitations as P2 also apply, this is a nested mode P2 over R |
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## Selection in terms of interoperability II
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| Mode | Base | Description |
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| :---: | :---------: | :---------: |
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| Mode | Base | Description |
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| :---: | :---------: | :----------------------------------------------------------------------------------------------------: |
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| F1 | Fakechroot | May escape and load host libraries. Requires shared library compiled against same libc as in container |
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| F2 | Fakechroot | Same as F1 |
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| F2 | Fakechroot | Same as F1 |
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| F3 | Fakechroot | Requires shared library compiled against same libc as in container. Binary executables and libraries get tied to the user HOME pathname |
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| F4 | Fakechroot | Same as F3. Executables and libraries can be compiled or added dynamically |
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| S1 | Singularity | Not part of `udocker` must already exist on the system, may use user namespaces or chroot |
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| F4 | Fakechroot | Same as F3. Executables and libraries can be compiled or added dynamically |
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| S1 | Singularity | Not part of `udocker` must already exist on the system, may use user namespaces or chroot |
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## `udocker` & Lattice QCD
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OpenQCD is a very advanced code to run lattice simulations
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OpenQCD is a very advanced code to run lattice simulations.
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Scaling performance as a function of the cores for the computation of application of the Dirac operator to a spinor field.
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Using OpenMPI, `udocker` in P1 mode
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Using OpenMPI, `udocker` in P1 mode.
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![bg right:40% w:550px](imgs/scaling.png)
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## `udocker` & `udocker` & Molecular dynamics
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## `udocker` & Molecular dynamics
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Gromacs is widely used both in biochemical and non-biochemical systems.
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Gromacs is widely used both in biochemical and non-biochemical systems.
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In this comparison Gromacs was run using CUDA and OpenMP
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In this comparison Gromacs was run using CUDA and OpenMP:
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* `udocker` using P mode has lower performance with Gromacs
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* `udocker` using P mode has lower performance with Gromacs.
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* `udocker` using F mode has same or better performance as Docker.
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![bg right:50% w:700px](imgs/ratio-gromacs.png)
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## `udocker` & Phenomenology
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MasterCode connects several complex codes. Hard to deploy. Scanning through large parameter spaces. High Throughput Computing.
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MasterCode connects several complex codes:
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* Hard to deploy.
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* Scanning through large parameter spaces.
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* High Throughput Computing.
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* C++, Fortran, many authors, legacy code.
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C++, Fortran, many authors, legacy code. Performance Degradation (*udocker in P1 mode*)
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Performance Degradation (*udocker in P1 mode*)
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| Environment | Compiling | Running |
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| :---------: | :-------: | :-----: |
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| HOST | 0% | 0% |
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| DOCKER | 10% | 1.0% |
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| udocker | 7% | 1.3% |
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| VirtualBox | 15% | 1.6% |
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| KVM | 5% | 2.6% |
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| HOST | 0% | 0% |
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| DOCKER | 10% | 1.0% |
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| udocker | 7% | 1.3% |
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| VirtualBox | 15% | 1.6% |
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| KVM | 5% | 2.6% |
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## Other container technologies
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* Singularity (LBL) - `udocker` currently supports it as execution mode
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* Charliecloud (LANL) - devels contacted Jorge: can `udocker` have a mode for it?
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"Merge" the `udocker`, CLI functionality with underlying Charliecloud engine?
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* Shifter (NERSC) - at the moment no plans on any type of usage/integration in `udocker`.
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* Podman (RedHat)
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* Singularity/Apptainer (LBL) <https://apptainer.org/> - `udocker` currently supports it as execution mode.
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* Charliecloud (LANL) <https://charliecloud.io/>.
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* Shifter (NERSC) <https://docs.nersc.gov/development/containers/shifter/how-to-use/>.
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* Podman (RedHat) <https://www.redhat.com/en/topics/containers/what-is-podman>.

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