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https://github.com/ndokmai/sgx-genotype-imputation
SMac: Genotype Imputation in Intel SGX
https://github.com/ndokmai/sgx-genotype-imputation
Last synced: about 1 month ago
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SMac: Genotype Imputation in Intel SGX
- Host: GitHub
- URL: https://github.com/ndokmai/sgx-genotype-imputation
- Owner: ndokmai
- Created: 2020-05-23T06:28:07.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2022-10-19T19:04:44.000Z (about 2 years ago)
- Last Synced: 2024-08-03T01:23:33.572Z (4 months ago)
- Language: Rust
- Homepage:
- Size: 105 MB
- Stars: 2
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- Awesome-SGX-Open-Source - https://github.com/ndokmai/sgx-genotype-imputation
README
# SMac: Secure Genotype Imputation in Intel SGX
## Installation Requirements
- Ubuntu 16.04/18.04
- [Rust Nightly](https://www.rust-lang.org/tools/install) (tested with version 1.56)
- To install the nightly channel, run
```bash
rustup toolchain install nightly
```
- [Fortanix EDP](https://edp.fortanix.com/docs/installation/guide/) (for running in SGX mode)
- For **Install AESM service**, we recommend installing the **Ubuntu 16.04/18.04** option. In addition, try installing
```bash
sudo apt install libsgx-ae*
```
Make sure AESM service is up and running by
```bash
sudo service aesmd status
```
- [Clang 3.8.0](https://releases.llvm.org/download.html) (for remote attestation)
- To automatically set up clang 3.8.0 locally, run `./setup_clang.sh`
## Two-sided rank-sum tests for timing leakage
To test whether SMac and SMac-lite's subroutines leak timing discrepancies, run
```bash
./test_leakage.sh
```
SMac-lite relies on `if-else` and `f32`, while SMac relies on `fixed-select` and `fixed-time-ln` for computation involving sensitive data. It is normal to observe leakage in `if-else` and `f32`, while `fixed-select` and `fixed-time-ln` should **NOT** leak.
## Configuration & Build
Edit the following parameters in [config.sh](config.sh) to configure SMac:
- `LITE`: SMac or SMac-lite
- `0`: SMac, with timing protection
- `1`: SMac-lite, without timing protection
- `SGX`: SGX or simulation mode
- `0`: simulation mode; no SGX hardware required
- `1`: SGX mode; Fortanix EDP must be installed and configured properly
- `RA`: remote attestation
- `0`: disable remote attestation
- `1`: enable remote attestation; this has not effect if `SGX=0`.
- `N_THREADS`: Number of threads for batch processing; 1 thread per 1 input.
- `ENCLAVE_HEAP_SIZE`: enclave heap size; if the enclave fails while starting, try increasing this number.
Rebuild for every change in configuration.
Next, build by running
```bash
./build.sh
```
### Remote attestation configuration
If remote attestation is enabled, follow the steps below to ensure access to Intel Attestation Service.
1. Sign up for a Development Access account at https://api.portal.trustedservices.intel.com/EPID-attestation. Make sure that the Name Base Mode is Linkable Quote. Take note of "SPID", "Primary key", and "Secondary key".
2. Modify the following fields in [client/settings.json](client/settings.json) using the information from the previous step:
- "spid": "\"
- "primary_subscription_key": "\"
- "secondary_subscription_key": "\"
## Quick Test
To locally test whether the code can run successfully according to the configuration, run
```bash
./test.sh
```
The script will test the code with all the sample data files located at [smac/test_data/](smac/test_data/). The outputs of SMac will be saved in [results/](results/).
## Workflow
```
+---------------------------------+
+-----------------------------+ | +--------+ |
| | | | | |
| Intel Attestation Service | | | Host | |
| | | | | |
+--------------^--------------+ | +----|---+ |
| | | |
| | reference panel | |
verify attestation | | | |
| network | +---------------|---------+ |
+---------|--------+ | | | | |
| | | | | +------------v------+ | |
| +-----v----+ | input | | | | | |
| | -----------------------------> Service Provider | | |
| | Client | | | | | | | |
| | <----------------------------- [running SMac] | | |
| +----------+ | output | | | | | |
| | | | +-------------------+ | |
+--Client Machine--+ | | | |
| +-------SGX Enclave-------+ |
| |
+-----------Host Machine----------+
```
## Client
### Input data format
SMac client takes two files as user input: bitmask file and symbol file. These two files together
encode a haplotype sequence that the user wishes to impute. Bitmast file includes a binary
vector (0 or 1 in each line) indicating whether the corresponding genetic variant in the
reference panel (M3VCF file) is included in the user's data. Note that the length of this
vector should match the number of genetic variants in the reference panel. Symbol file includes
a vector of -1 (missing), 0 (reference allele), or 1 (alternative allele), one for each line.
These correspond to the user's data values at the nonzero indices in the index file.
Example input files (`input_ind.txt` and `input_dat.txt`) as well as sample scripts for
generating random input can be found in [scripts/](scripts/).
### Running Client
To start Client on Client Machine, run
```bash
./run_client.sh
```
where `` are formatted according to [input data format](#input-data-format). `` is a directory containing all symbol files for batch processing, and `` is a directly to save results. For example,
```bash
./run_client.sh 127.0.0.1 smac/test_data/large_input_bitmask.txt smac/test_data/batch results
```
## Service Provider
SMac service provider takes the reference panel in the M3VCF format as input. To start Service Provider and Host on Host Machine,
```bash
./run_sp.sh
```
where `` is a reference panel gzipped M3VCF file. For example,
```bash
./run_sp.sh smac/test_data/largeref.m3vcf.gz
```
## Output format
The output of SMac is a text file including the imputed alternative allele dosages at every
genetic position covered by the reference panel M3VCF file (one number per line).
## Contact for questions
Ko Dokmai, [email protected]
Hoon Cho, [email protected]