Caffe

Caffe is a deep learning framework developed with cleanliness, readability, and speed in mind.

Running Caffe (master branch Jan 29, 2016) on Copper and Mosaic

Sharcnet doesn't maintain Caffe as a module, but we provide all its dependencies and a precompiled Caffe as an example.

All the files that needed to build and run Caffe are under:

/opt/sharcnet/testing/caffe

Setting up modules and environment variables

There is a script (caffe-set-env.sh) that can help setup all the modules and environment variables:

module unload intel gcc mkl openmpi hdf python cuda
module load intel/15.0.3
module load hdf/serial/5.1.8.11
module load cuda/7.5.18
module load python/intel/2.7.10
export CAFFE_ROOT=/opt/sharcnet/testing/caffe/caffe-master-160129
export PATH=/opt/sharcnet/testing/caffe/caffe-libs/bin:/opt/sharcnet/testing/caffe/caffe-libs/include:/opt/sharcnet/testing/cudnn/cudnn3:$PATH
export LD_LIBRARY_PATH=/opt/sharcnet/testing/caffe/caffe-libs/lib:/opt/sharcnet/testing/cudnn/cudnn3:$LD_LIBRARY_PATH
export PYTHONPATH=/opt/sharcnet/testing/caffe/caffe-libs/lib/python2.7/site-packages:/opt/sharcnet/testing/caffe/caffe-master-160129/python:$PYTHONPATH

In this file, CAFFE_ROOT is set to a precompiled Caffe which was built on Jan 29th, 2016. If you want to use this version of caffe, you don't have to run the commands above, you can simply do:

source /opt/sharcnet/testing/caffe/caffe-set-env.sh

• You should run this command every time you login to a sharcnet system, or put it into your .bashrc if you really know what these commands will do.

Preparing data set (e.g. Imagenet)

Although Caffe can take images directly as an input, for a better I/O performance, LMDB database is strongly recommended. Caffe provides a tool and a script to build lmdb database from images. You should copy the script to your place and modify it to meet your own needs. The script is

$CAFFE_ROOT/examples/imagenet/create_imagenet.sh

In this file, there are some variables you should modify:

• EXAMPLE, should be a folder that you want to storage the lmdb database file.

EXAMPLE=/work/yourname/imagentet/lmdb

• DATA, should be a folder where you keep the label files, train.txt and val.txt

DATA=/work/yourname/imagenet/labels

• TOOLS, should be tools folder in Caffe, here we use the precompiled Caffe as an example

TOOLS=$CAFFE_ROOT/build/tools

• TRAIN_DATA_ROOT and VAL_DATA_ROOT, should be folders that contains your images (e.g. .jpg files)

TRAIN_DATA_ROOT=/work/yourname/imagenet/train/
VAL_DATA_ROOT=/work/yourname/imagenet/val/

• RESIZE, should be set to true if you haven't resized the images to 256x256
• In the train.txt and val.txt, you should specify the image names with locations and lables. For example:

n01440764/n01440764_10254.JPEG 0
n01440764/n01440764_10281.JPEG 0

Each line contains one image location and label. "n01440764" is the subfolder's name under $TRAIN_DATA_ROOT. The full path to this image should be /work/yourname/imagenet/train/n01440764/n01440764_10254.JPEG

• You can use data/ilsvrc12/get_ilsvrc_aux.sh script in Caffe to download the labels for imagenet.

After building the LMDB database, we should also compute an image mean file (imagenet_mean.binaryproto) based on the data you have. The script is $CAFFE_ROOT/examples/imagenet/make_imagenet_mean.sh. You should modify the variables inside to the same as we modified in create_imagenet.sh. If you have run the get_ilsvrc_aux.sh, an imagenet_mean.binaryproto which was computed on imagenet dataset will be downloaded.

Define models (Alexnet as an example)

Caffe provides an Alexnet model in $CAFFE_ROOT/models/bvlc_alexnet. Here we copy this folder to /home or /work so that we can modify it. First we should modify "train_val.prototxt" file. We should change the "mean_file" to where we hold the image mean. And the "source" for training and validation.

name: "AlexNet"
layer {
  name: "data"
  type: "Data"
  top: "data"
  top: "label"
  include {
    phase: TRAIN
  }
  transform_param {
    mirror: true
    crop_size: 227
    mean_file: "/work/feimao/imagenet/imagenet_mean.binaryproto"
  }
  data_param {
    source: "/work/feimao/imagenet/ilsvrc12_train_lmdb"
    batch_size: 256
    backend: LMDB
  }
}
layer {
  name: "data"
  type: "Data"
  top: "data"
  top: "label"
  include {
    phase: TEST
  }
  transform_param {
    mirror: false
    crop_size: 227
    mean_file: "/work/feimao/imagenet/imagenet_mean.binaryproto"
  }
  data_param {
    source: "/work/feimao/imagenet/ilsvrc12_val_lmdb"
    batch_size: 50
    backend: LMDB
  }
}

And then changing the solver.prototxt to located the train_val.prototxt file and the output snapshot.

net: "/work/feimao/imagenet/bvlc_alexnet/train_val.prototxt"
test_iter: 1000
test_interval: 1000
base_lr: 0.01
lr_policy: "step"
gamma: 0.1
stepsize: 100000
display: 20
max_iter: 450000
momentum: 0.9
weight_decay: 0.0005
snapshot: 10000
snapshot_prefix: "/work/feimao/imagenet/bvlc_alexnet/caffe_alexnet_train"
solver_mode: GPU

Caffe (master branch Dec 3, 2015) with cudnn v3(CUDA7.5) on Copper and Mosaic

All Copper and Mosaic nodes have the latest CUDA 7.5.

The caffe dependency libraries are under /work/feimao/software_installs/caffe-new/caffe-libs and /work/feimao/software_installs/cudnn3, you can use this folder directly or copy it somewhere under your folder(e.g. /work/yourname/caffe-libs and/work/yourname/cudnn3 ) If you don't need to compile your own Caffe, you can simply copy the one from:/work/feimao/software_installs/caffe-new/caffe-master-1203-75-python2710, which was built on Dec 3, 2015.

How to run a precompiled Caffe

To run the program, you should put caffe-libs and caffe-master-1203-75-python2710 under you folder, and then load the modules and export the environment paths:

module unload intel/12.1.3 mkl/10.3.9 openmpi/intel/1.6.2
module load intel/15.0.3
module load hdf/serial/5.1.8.11 
module unload cuda
module load cuda/7.5.18 
module load python/intel/2.7.10
export PATH=/work/yourname/caffe-libs/bin:/work/yourname/caffe-libs/include:/work/yourname/cudnn3:$PATH
export LD_LIBRARY_PATH=/work/yourname/caffe-libs/lib:/work/yourname/cudnn3:$LD_LIBRARY_PATH
export PYTHONPATH=/work/yourname/caffe-libs/lib/python2.7/site-packages:/work/yourname/caffe-master-1203-75-python2710/python:$PYTHONPATH

How to build Caffe

If you'd like to build your own Caffe, you can simply get the newest Caffe from github (notice that you should stay in login node to have internet access):

[feimao@mos-login test-install-caffe]$ git clone https://github.com/BVLC/caffe.git

You should also prepaired all Caffe's dependency libraries. Just copy the folder /work/feimao/software_installs/caffe-new/caffe-libs/ and /work/feimao/software_installs/cudnn3 to somewhere under your folder (e.g. /work/yourname/caffe-libs and /work/yourname/cudnn3 ) Then you go to mos1 (or cop1), load the modules:

module unload intel/12.1.3 mkl/10.3.9 openmpi/intel/1.6.2
module load intel/15.0.3
module load hdf/serial/5.1.8.11 
module unload cuda
module load cuda/7.5.18 
module load python/intel/2.7.10

And export the environment paths to your caffe-libs folder:

export PATH=/work/yourname/caffe-libs/bin:/work/yourname/caffe-libs/include:/work/yourname/cudnn3:$PATH
export LD_LIBRARY_PATH=/work/yourname/caffe-libs/lib:/work/yourname/cudnn3:$LD_LIBRARY_PATH
export PYTHONPATH=/work/yourname/caffe-libs/lib/python2.7/site-packages:$PYTHONPATH

and go to the Caffe folder and copy the Makefile.config.example to Makefile.config:

[feimao@mos1 caffe]$ cp Makefile.config.example Makefile.config

Then modify the Makefile.config:

• 1, uncomment

USE_CUDNN := 1

• 2, uncomment

CUSTOM_CXX := g++

• 3, change CUDA_DIR to

CUDA_DIR := /opt/sharcnet/cuda/7.5.18

• 4, If on Copper, add a line "-gencode arch=compute_37,code=sm_37" to CUDA_ARCH
• 5, change BLAS to

BLAS := mkl

• 6, uncomment BLAS_INCLUDE, and change to

BLAS_INCLUDE := /opt/sharcnet/intel/15.0.3/mkl/include

• 7, uncomment BLAS_LIB, and change to

BLAS_LIB := /opt/sharcnet/intel/15.0.3/mkl/lib/intel64

• 8, change PYTHON_INCLUDE to

PYTHON_INCLUDE := /opt/sharcnet/python/2.7.10/intel/include \
                /opt/sharcnet/python/2.7.10/intel/include/python2.7 \
               /opt/sharcnet/python/2.7.10/intel/lib/python2.7/site-packages/numpy/core/

• 9, change PYTHON_LIB to

PYTHON_LIB := /opt/sharcnet/python/2.7.10/intel/lib

• 10, change INCLUDE_DIRS to

INCLUDE_DIRS := $(PYTHON_INCLUDE) /opt/sharcnet/hdf/5.1.8.11/serial/include /work/yourname/caffe-libs/include /work/yourname/cudnn3 /usr/local/include

• 10, change LIBRARY_DIRS to

LIBRARY_DIRS := $(PYTHON_LIB) /opt/sharcnet/hdf/5.1.8.11/serial/lib /work/yourname/caffe-libs/lib /work/yourname/cudnn3 /usr/local/lib /usr/lib

• 11, run command to build Caffe and pycaffe:

make all -j8 && make test -j8 && make pycaffe

How to test the Caffe build

When the "make all" and "make test" finish, you can run "make runtest" to test if you build Caffe properly. You may get errors related to "test_gradient_based_solver.cpp" or other numerical inconsistency between CPU and GPU. Those errors was caused by MKL's Conditional Numerical Reproducibility setting. To avoid these errors, you should set MKL_CBWR:

export MKL_CBWR=AUTO

If you use GPU, you don't have to set this during the calculation.

Mosaic cluster installation instructions for Caffe with cudnn v2

You can copy dependencies from

/work/feimao/software_installs/caffe-mosaic/caffe-libs

to somewhere under your folder, OR use these files from their original path directly. You can download cuDNN v2, or copy from /work/feimao/software_installs/cudnn2

Copy compiled Caffe folder for mosaic with cudnn v2 support from:

/work/feimao/software_installs/caffe-mosaic/caffe-master-0717-mosaic-65-python

To run the program, you should do

module unload intel mkl openmpi
module load gcc/4.9.2
module load python/gcc/2.7.8
module switch cuda/6.0.37 cuda/6.5.14

You should also export environment path (can be your folder, including where you put cuDNN v2) using command below:

export LD_LIBRARY_PATH=/work/feimao/software_installs/cudnn2:/work/feimao/software_installs/caffe-mosaic/caffe-libs:/opt/sharcnet/cuda/6.5.14/toolkit/lib64/:$LD_LIBRARY_PATH

export the ptyhon path as well:

export PYTHONPATH=/work/feimao/software_installs/caffe-mosaic/caffe-libs/python_packages/lib/python2.7/site-packages:/work/feimao/software_installs/caffe-mosaic/caffe-master-0717-mosaic-65-python/python:$PYTHONPATH

If you want to compile caffe by your self, you should also export the path above to PATH variable(export PATH=/work/feimao/software_installs/caffe-mosaic/caffe-libs:$PATH). And modify the Makefile and Makefile.config as the ones in "caffe-master-0717-mosaic-65-python" folder. If you need help with the installation or using caffe, please email help@sharcnet.ca or submit a ticket.

SHARCNET installation instructions for old version of Caffe

Building Caffe and its dependencies on SHARCNET is not an easy job. If you are not willing to change/modify Caffe's source file, you can copy the Caffe and its dependencies from /work/feimao/software_installs/ directories to yours.

The paths to all dependencies:

Protobuf: /work/feimao/software_installs/protobuf
LevelDB: /work/feimao/software_installs/leveldb
Snappy: /work/feimao/software_installs/snappy
OpenCV(for cuda 6 on monk): /work/feimao/software_installs/opencv
OpenCV(for cuda6.5 on angel): /work/feimao/software_installs/opencv65
Boost(with python 2.7.8 support): /work/feimao/software_installs/boost/boost_157_2
Gflags: /work/feimao/software_installs/gflags
Glog: /work/feimao/software_installs/glog
LMDB: /work/feimao/software_installs/lmdb
cuDNN: /work/feimao/software_installs/cudnn

There are two version of Caffe, one for Monk, one for Angel(with newer 750Ti gpu).

Monk version is build with cuda6 and python support(no cudnn):

/work/feimao/software_installs/caffe/caffe-monk-cuda6-python

Angel version is build with cuda 6.5 with cudnn support:

/work/feimao/software_installs/caffe/caffe-angel-cuda65-cudnn

Setting up the environment for Caffe (old version)

To run caffe, you should load the gcc module first:

module unload intel/12.1.3 mkl/10.3.9 openmpi/intel/1.6.2 
module load gcc/4.8.2

Then export the PATH and LD_LIBRARY_PATH: For Monk:

export PATH=/work/feimao/software_installs/cudnn:/work/feimao/software_installs/opencv/include:/work/feimao/software_installs/opencv/bin:/work/feimao/software_installs/boost/boost_157_2/include:/work/feimao/software_installs/lmdb/include/:/work/feimao/software_installs/lmdb/bin/:/work/feimao/software_installs/leveldb/leveldb-1.15.0:/work/feimao/software_installs/lmdb/mdb-mdb/libraries/liblmdb/:/work/feimao/software_installs/lmdb/bin:/work/feimao/software_installs/lmdb/include:/work/feimao/software_installs/glog/include/:/work/feimao/software_installs/gflags/include/:/work/feimao/software_installs/protobuf/bin/:/work/feimao/software_installs/snappy/include/:$PATH

export LD_LIBRARY_PATH=/work/feimao/software_installs/cudnn:/work/feimao/software_installs/opencv/lib:/work/feimao/software_installs/boost/boost_157_2/lib:/work/feimao/software_installs/lmdb/mdb-mdb/libraries/liblmdb/:/work/feimao/software_installs/lmdb/lib/:/work/feimao/software_installs/leveldb/leveldb-1.15.0:/work/feimao/software_installs/protobuf/lib/:/work/feimao/software_installs/gflags/lib:/work/feimao/software_installs/glog/lib/:/work/feimao/software_installs/snappy/lib/:$LD_LIBRARY_PATH

For Angel:

export PATH=/work/feimao/software_installs/cudnn:/work/feimao/software_installs/opencv65/include:/work/feimao/software_installs/opencv65/bin:/work/feimao/software_installs/boost/boost_157_2/include:/work/feimao/software_installs/lmdb/include/:/work/feimao/software_installs/lmdb/bin/:/work/feimao/software_installs/leveldb/leveldb-1.15.0:/work/feimao/software_installs/lmdb/mdb-mdb/libraries/liblmdb/:/work/feimao/software_installs/lmdb/bin:/work/feimao/software_installs/lmdb/include:/work/feimao/software_installs/glog/include/:/work/feimao/software_installs/gflags/include/:/work/feimao/software_installs/protobuf/bin/:/work/feimao/software_installs/snappy/include/:$PATH

export LD_LIBRARY_PATH=/work/feimao/software_installs/cudnn:/work/feimao/software_installs/opencv65/lib:/work/feimao/software_installs/boost/boost_157_2/lib:/work/feimao/software_installs/lmdb/mdb-mdb/libraries/liblmdb/:/work/feimao/software_installs/lmdb/lib/:/work/feimao/software_installs/leveldb/leveldb-1.15.0:/work/feimao/software_installs/protobuf/lib/:/work/feimao/software_installs/gflags/lib:/work/feimao/software_installs/glog/lib/:/work/feimao/software_installs/snappy/lib/:$LD_LIBRARY_PATH

ImageNet example on Angel and Monk

For training AlexNet on ImageNet dataset, you should download the images first and put them into "data" folder under caffe root. Then go to "examples/imagenet/" and modify create_imagenet.sh by adding "--backend=leveldb" and change the name from lmdb to leveldb for both "train" and "val" data like this:

GLOG_logtostderr=1 $TOOLS/convert_imageset \
    --resize_height=$RESIZE_HEIGHT \
    --resize_width=$RESIZE_WIDTH \
    --shuffle \
    --backend=leveldb \
    $TRAIN_DATA_ROOT \
    $DATA/train.txt \
   $EXAMPLE/ilsvrc12_train_leveldb

Then you should also modify the "train_val.prototxt" under "models/bvlc_alexnet". You have to change "LMDB" to "LEVELDB" and fix the path to the leveldb database.

data_param {
    source: "examples/imagenet/ilsvrc12_train_leveldb"
    backend: LEVELDB
    batch_size: 256
  }

If running on Angel, you should set a smaller batch_size if you get "out of memory" error. It is caused by the small amount of RAM on the GTX 750Ti(2GB).

After changing the parameters in solver.prototxt, you should be able to run Caffe now.

To submit a job, you should setup a properaiat memory size which is large enough for you network size.

sqsub -q gpu --gpp=1 --mpp=24g -r 24h -o out.txt ./build/tools/caffe train --solver=models/bvlc_alexnet/solver.prototxt

Bug on Monk

The GPU on Monk is relatively old and with only SM2.0 support. For large networks, it will be running out of blocks per grid dim (SM 2.0 had only 65535 blocks per dim, while 3.0 bumped it to 2^31-1). This will happen when using AlexNet. There is no official fix for this problem yet. Based on this webpage[1], I modifed the code in "include/util/device_alternate.hpp" to

// CUDA: number of blocks for threads.
inline int CAFFE_GET_BLOCKS(const int N) {
int num_blocks = (N + CAFFE_CUDA_NUM_THREADS - 1) / CAFFE_CUDA_NUM_THREADS;
//return (N + CAFFE_CUDA_NUM_THREADS - 1) / CAFFE_CUDA_NUM_THREADS;
if (num_blocks > 65535)
{
        num_blocks=65535;
}
return num_blocks;//deal with sm20 devices
}

}  // namespace caffe

== References ===