How to Zip Folder That Contains More Than 12Gb Data

zip command skip errors

tar is always a good option to compress in Linux. Beware that zip may also have file size limit issue.

tar vcfz file.tar.gz folder

Jersey Client download ZIP file and unpack efficiently

Ok so I solved it, apparently my request was getting a 404 for adding the query param in the path... .path("download?delete=true")

Check the total content size of a tar gz file

This will sum the total content size of the extracted files:

$ tar tzvf archive.tar.gz | sed 's/ \+/ /g' | cut -f3 -d' ' | sed '2,$s/^/+ /' | paste -sd' ' | bc

The output is given in bytes.

Explanation: tar tzvf lists the files in the archive in verbose format like ls -l. sed and cut isolate the file size field. The second sed puts a + in front of every size except the first and paste concatenates them, giving a sum expression that is then evaluated by bc.

Note that this doesn't include metadata, so the disk space taken up by the files when you extract them is going to be larger - potentially many times larger if you have a lot of very small files.

Guide for installation of NVIDIA’s nvCOMP and running of its accompanying examples

I will answer my own question.

System info

Here is the system information obtained from the command line:

uname -r: 5.15.0-46-generic
lsb_release -a: Ubuntu 20.04.5 LTS
nvcc --version: Cuda compilation tools, release 10.1, V10.1.243
nvidia-smi:
- Two Tesla K80 (2-in-1 card) and one GeForce (Gigabyte RTX 3060 Vision 12G rev . 2.0)
- NVIDIA-SMI 470.82.01
- Driver Version: 470.82.01
- CUDA Version: 11.4
cmake --version: cmake version 3.22.5
make --version: GNU Make 4.2.1
lscpu: Xeon CPU E5-2680 V4 @ 2.40GHz - 56 CPU(s)

Observation

Although there are two GPUs installed in the server, nvCOMP only works with the RTX.

The Steps

Perhaps "installation" is a misnomer. One only needs to properly compile the downloaded nvCOMP files and run the resulting executables.

Step 1: The nvCOMP library

Download the nvCOMP library from https://developer.nvidia.com/nvcomp.

The file I downloaded was named nvcomp_install_CUDA_11.x.tgz. And I left the extracted folder in the Downloads directory and renamed it nvcomp.

Step 2: The nvCOMP test package on GitHub

Download it from https://github.com/NVIDIA/nvcomp. Click the green "Code" icon, then click "Download ZIP".

By default, the downloaded zip file is called nvcomp-main.zip. And I left the extracted folder, named nvcomp-main, in the Downloads directory.

Step 3: The NIVIDIA CUB library on GitHub

Download it from https://github.com/nvidia/cub. Click the green "Code" icon, then click "Download ZIP".

By default, the downloaded zip file is called cub-main.zip. And I left the extracted folder, named cub-main, in the Downloads directory.

There is no "installation" of the CUB library other than making the folder path "known", ie available, to the calling program.

Comments: The nvCOMP GitHub site did not seem to explain that the CUB library was needed to run nvCOMP, and I only found that out from an error message during an attempted compilation of the test files in Step 2.

Step 4: "Building CPU and GPU Examples, GPU Benchmarks provided on Github"

The nvCOMP GitHub landing page has a section with the exact name as this Step. The instructions could have been more detailed.

Step 4.1: cmake

All in the Downloads directory are the folders nvcomp(the Step 1 nvCOMP library), nvcomp-main (Step 2), and cub-main (Step 3).
Start a terminal and then go inside nvcomp-main, ie, go to /your-path/Downloads/nvcomp-main
Run cmake -DCMAKE_PREFIX_PATH=/your-path/Downloads/nvcomp -DCUB_DIR=/your-path/Downloads/cub-main
This cmake step sets up the build files for the next make" step.
During cmake, a harmless yellow-colored cmake warning appeared
There was also a harmless printout "-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed" per this thread.
The last few printout lines from cmake variously stated it found Threads, nvcomp, ZLIB (on my system) and it was done with "Configuring" and "Build files have been written".

Step 4.2: make

Run make in the same terminal as above.
This is a screenshot of the make compilation.
Please check the before and after folder tree to see what files have been generated.

Step 5: Running the examples/benchmarks

Let's run the "built-in" example before running the benchmarks with the (now outdated) Fannie Mae single-family loan performance data from NVIDIA's RAPIDS repository.

Check if there are executables in /your-path/Downloads/nvcomp-main/bin. These are the excutables created from the cmake and make steps above.

You can try to run these executables on your to-be-compressed files, which are buit with different compression algorithms and functionalities. The name of the executable indicates the algorithm used and/or its functionality.

Some of the executables require the files to be of a certain size, eg, the "benchmark_cascaded_chunked" executable requires the target file's size to be a multiple of 4 bytes. I have not tested all of these executables.

Step 5.1: CPU compression examples

Per https://github.com/NVIDIA/nvcomp
Start a terminal (anywhere)
Run time /your-path/Downloads/nvcomp-main/bin/gdeflate_cpu_compression -f /full-path-to-your-target/my-file.txt
Here are the results of running gdeflate_cpu_compression on an updated Fannie Mae loan data file "2002Q1.csv" (11GB)
Similarly, change the name of the executable to run lz4_cpu_compression or lz4_cpu_decompression

Step 5.2: The benchmarks with the Fannie Mae files from NVIDIA Rapids

Apart from following the NVIDIA instructions here, it seems the "benchmark" executables in the above "bin" directory can be run with "any" file. Just use the executable in the same way as in Step 5.1 and adhere to the particular executable specifications.

Below is one example following the NVIDIA instruction.

Long story short, the nvcomp-main(Step 2) test package contains the files to (i) extract a column of homogeneous data from an outdated Fannie Mae loan data file, (ii) save the extraction in binary format, and (iii) run the benchmark executable(s) on the binary extraction.

The Fannie Mae single-family loan performance data files, old or new, all use "|" as the delimiter. In the outdated Rapids version, the first column, indexed as column "0" in the code (zero-based numbering), contains the 12-digit loan IDs for the loans sampled from the (real) Fannie Mae loan portfolio. In the new Fannie Mae data files from the official Fannie Mae site, the loan IDs are in column 2 and the data files have a csv file extension.

Download the dataset "1 Year" Fannie Mae data, not the "1GB Splits*" variant, by following the link from here, or by going directly to RAPIDS
Place the downloaded mortgage_2000.tgz anywhere and unzip it with tar -xvzf mortgage_2000.tgz.
There are four txt files in /mortgage_2000/perf. I will use Performance_2000Q1.txt as an example.
Check if python is installed on the system
Check if text_to_binary.py is in /nvcomp-main/benchmarks
Start a terminal (anywhere)
As shown below, use the python script to extract the first column, indexed "0", with format long, from Performance_2000Q1.txt, and put the .bin output file somewhere.
- Run time python /your-path/Downloads/nvcomp-main/benchmarks/text_to_binary.py /your-other-path-to/mortgage_2000/perf/Performance_2000Q1.txt 0 long /another-path/2000Q1-col0-long.bin
- For comparison of the benchmarks, run time python /your-path/Downloads/nvcomp-main/benchmarks/text_to_binary.py /your-other-path-to/mortgage_2000/perf/Performance_2000Q1.txt 0 string /another-path/2000Q1-col0-string.bin
Run the benchmarking executables with the target bin files as shown at the bottom of the web page of the NVIDIA official guide
- Eg, /your-path/Downloads/nvcomp-main/bin/benchmark_hlif lz4 -f /another-path/2000Q1-col0-long.bin
- Just make sure the operating system know where the executable and the target file are.

Step 5.3: The high_level_quickstart_example and low_level_quickstart_example

These two executables are in /nvcomp-main/bin
They are completely self contained. Just run eg high_level_quickstart_example without any input arguments. Please see corresponding c++ source code in /nvcomp-main/examples and see the official nvCOMP guides on GitHub.

Observations after some experiments

This could be another long thread but let's keep it short. Note that NVIDIA used various A-series cards for its benchmarks and I used a GeForce RTX 3060.

Speed

The python script is slow. It took 4m12.456s to extract the loan ID column from an 11.8 GB Fannie Mae data file (with 108 columns) using format "string"
In contract, R with data.table took 25.648 seconds to do the same.
With the outdated "Performance_2000Q1.txt" (0.99 GB) tested above, the python script took 32.898s whereas R took 26.965s to do the same extraction.

Compression ratio

"Bloated" python outputs.
- The R-output "string.txt" files are generally a quarter of the size of the corresponding python-output "string.bin" files.
Applying the executables to the R-output files achieved much better compression ratio and throughputs than to the python-output files.
- Eg, running benchmark_hlif lz4 -f 2000Q1-col0-string.bin with the python output vs running benchmark_hlif lz4 -f 2000Q1-col0-string.txt with the R output
- Uncompressed size: 436,544,592 vs 118,230,827 bytes
- Compressed size: 233,026,108 vs 4,154,261 bytes
- Compressed ratio: 1.87 vs 28.46 bytes
- Compression throughput (GB/s): 2.42 vs 18.96
- decompression throughput (GB/s): 8.86 vs 91.50
- Wall time: 2.805 vs 1.281s

Overall performance: accounting for file size and memory limits

Use of the nvCOMP library is limited by the GPU memory, no more than 12GB for the RTX 3060 tested. And depending on the compression algorithm, an 8GB target file can easily trigger a stop with cudaErrorMemoryAllocation: out of memory
In both speed and compression ratio, pigz trumped the tested nvCOMP excutables when the target files were the new Fannie Mae data files containing 108 columns of strings and numbers.