для конкретного анализа данных c, я использую предварительно скомпилированный двоичный файл ica_linux из этого хранилища . В README.md этого репозитория авторы утверждают, что вы можете добиться значительного ускорения при компиляции двоичного файла с архитектурой, определенной c реализациями BLAS / LAPACK. В нашем случае ускорение может фактически сэкономить дни вычислительного времени, поэтому я очень хочу скомпилировать файл с соответствующими библиотеками. Сейчас у меня нет большого опыта работы с make-файлами, поэтому я немного запутался в этом процессе - вот почему я прошу вашей помощи.
Моя система - сервер HP ProLiant d360 с два дека-ядерных процессора Intel Xeon E5-2650 v3 и Ubuntu 16.04.6 x64
Я попробовал следующее
клон репо
sudo git clone https://github.com/sccn/binica
cd binica
установить Intel MKL
Я использовал это руководство .
sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
sudo rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
sudo wget https://apt.repos.intel.com/setup/intelproducts.list -O /etc/apt/sources.list.d/intelproducts.list
sudo apt update
sudo apt install intel-mkl-2020.0-088
настроить Makefile. linux
Здесь я не совсем понимаю, какие у меня библиотеки добавить. Я попробовал следующее, но я не уверен, что это правильный путь.
PLAT = _linux
CC = gcc
CFLAGS = -O3 -ansi
#BLASLIB = ./CLAPACK/lsblaspii1.2f_03.00.a
#BLASLIB = ./CLAPACK/blas$(PLAT).a
#LAPACKLIB = ./CLAPACK/lapack$(PLAT).a
#F2CLIB = ./CLAPACK/F2CLIBS/libF77$(PLAT).a ./CLAPACK/F2CLIBS/libI77$(PLAT).a
#LIBS = $(LAPACKLIB) $(BLASLIB) $(F2CLIB) -lm
LIBS = /opt/intel/mkl/lib/intel64_lin/libmkl_intel_ilp64.a
OBJS = ica.o interfc.o r250.o randlcg.o dsum.o
ica_linux: Makefile.linux ica.h memap.h $(OBJS)
$(CC) -o ica_linux $(OBJS) $(LIBS)
ica.o: Makefile.linux ica.h memap.h ica.c
$(CC) -c ica.c $(CFLAGS)
interfc.o: Makefile.linux ica.h memap.h interfc.c
$(CC) -c interfc.c $(CFLAGS)
memap.o: Makefile.linux memap.h memap.c
$(CC) -c memap.c $(CFLAGS)
r250.o: Makefile.linux r250.h r250.c
$(CC) -c r250.c $(CFLAGS)
randlcg.o: Makefile.linux randlcg.h randlcg.c
$(CC) -c randlcg.c $(CFLAGS)
dsum.o: Makefile.linux dsum.c
$(CC) -c dsum.c $(CFLAGS)
clean:
rm -f *.o
make file
Затем я запустил
sudo make Makefile.linux clean
sudo make Makefile.linux ica_linux
К сожалению, не с этим сообщением об ошибке:
```
X@Y:~/Downloads/binica$ sudo make Makefile.linux ica_linux
make: Nothing to be done for 'Makefile.linux'.
gcc -c ica.c -O3 -ansi
ica.c: In function ‘sigproc’:
ica.c:565:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘integer {aka long int}’ [-Wformat=]
printf("number of components = %d\n",COMP_NUMBER);
^
ica.c:566:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘integer {aka long int}’ [-Wformat=]
printf("number of channels = %d\n",CH_NUMBER);
^
ica.c: In function ‘runica’:
ica.c:904:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘integer {aka long int}’ [-Wformat=]
printf("step %d - lrate %5f, wchange %7.6f, angledelta %4.1f deg\n",step,lrate,change,DEGCONST*angledelta);
^
ica.c:907:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘integer {aka long int}’ [-Wformat=]
printf("step %d - lrate %5f, wchange %7.6f, angledelta %4.1f deg, %d subgauss\n",step,lrate,change,DEGCONST*angledelta,j);
^
ica.c:907:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘integer {aka long int}’ [-Wformat=]
ica.c:914:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘integer {aka long int}’ [-Wformat=]
printf("step %d - lrate %5f, wchange %7.6f\n",step,lrate,change);
^
ica.c:917:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘integer {aka long int}’ [-Wformat=]
printf("step %d - lrate %5f, wchange %7.6f, %d subgauss\n",step,lrate,change,j);
^
ica.c:917:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘integer {aka long int}’ [-Wformat=]
gcc -c interfc.c -O3 -ansi
interfc.c:50:17: warning: missing terminating " character
#define HELPMSG "# ica - Perform Independent Component Analysis, standalone-version
^
interfc.c:52:5: error: invalid preprocessing directive #Run
# Run the ICA algorithm of Bell & Sejnowski (1996) or the extended-ICA
^
interfc.c:53:5: error: invalid preprocessing directive #of
# of Lee, Girolami & Sejnowski (1998). Original Matlab code: Scott Makeig,
^
interfc.c:54:5: error: invalid preprocessing directive #Tony
# Tony Bell, et al.; C++ code: Sigurd Enghoff, CNL / Salk Institute 7/98
^
interfc.c:56:5: error: invalid preprocessing directive #Usage
# Usage: % ica < my.sc
^
interfc.c:58:5: error: invalid preprocessing directive #Leading
# Leading # -> use default values
^
interfc.c:59:5: error: invalid preprocessing directive #Edit
# Edit a copy of this file to run an ica decomposition
^
interfc.c:60:5: error: invalid preprocessing directive #Contacts
# Contacts: {enghoff,scott,terry,tony,tewon}@salk.edu
^
interfc.c:62:3: error: invalid preprocessing directive #Required
# Required variables:
^
interfc.c:63:5: error: unknown type name ‘DataFile’
DataFile berger/modeldata # Input data to decompose (floats multiplexed
^
interfc.c:63:24: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘/’ token
DataFile berger/modeldata # Input data to decompose (floats multiplexed
^
interfc.c:63:35: error: stray ‘#’ in program
DataFile berger/modeldata # Input data to decompose (floats multiplexed
^
interfc.c:64:32: error: invalid preprocessing directive #by
# by channel (i.e., chan1, chan2, ...))
^
interfc.c:65:28: error: stray ‘#’ in program
chans 31 # Number of data channels (= data rows)
^
interfc.c:66:28: error: stray ‘#’ in program
frames 768 # Number of data points per epoch (= data columns)
^
interfc.c:67:28: error: stray ‘#’ in program
epochs 436 # Number of epochs
^
interfc.c:69:3: error: invalid preprocessing directive #FrameWindow
# FrameWindow 20 # Number of frames per window
^
interfc.c:70:3: error: invalid preprocessing directive #FrameStep
# FrameStep 4 # Number of frames to step per window
^
interfc.c:71:3: error: invalid preprocessing directive #EpochWindow
# EpochWindow 100 # Number of epochs per window
^
interfc.c:72:3: error: invalid preprocessing directive #EpochStep
# EpochStep 25 # Number of epochs to step per window
^
interfc.c:73:3: error: invalid preprocessing directive #Baseline
# Baseline 25 # Number of data points contained in baseline
^
interfc.c:75:36: error: stray ‘#’ in program
WeightsOutFile berger/data.wts # Output ICA weight matrix (floats)
^
interfc.c:76:35: error: stray ‘#’ in program
SphereFile berger/data.sph # Output sphering matrix (floats)
^
interfc.c:78:3: error: invalid preprocessing directive #Processing
# Processing options:
^
interfc.c:80:5: error: invalid preprocessing directive #sphering
# sphering on # Flag sphering of data (on/off) {default: on}
^
interfc.c:81:5: error: invalid preprocessing directive #bias
# bias on # Perform bias adjustment (on/off) {default: on}
^
interfc.c:82:5: error: stray ‘\’ in program
\exextended 1 # Perform \"extended-ICA\" using tnah() with kurtosis
^
interfc.c:82:31: error: stray ‘#’ in program
\exextended 1 # Perform \"extended-ICA\" using tnah() with kurtosis
^
interfc.c:82:5: error: stray ‘\’ in program
\exextended 1 # Perform \"extended-ICA\" using tnah() with kurtosis
^
interfc.c:82:42: warning: missing terminating " character
\exextended 1 # Perform \"extended-ICA\" using tnah() with kurtosis
^
interfc.c:82:5: error: missing terminating " character
\exextended 1 # Perform \"extended-ICA\" using tnah() with kurtosis
^
interfc.c:83:31: error: invalid preprocessing directive #estimation
# estimation every N training blocks. If N < 0,
^
interfc.c:84:31: error: invalid preprocessing directive #fix
# fix number of sub-Gaussian components to -N
^
interfc.c:85:31: error: invalid preprocessing directive #{
# {default|0: off}
^
interfc.c:86:5: error: invalid preprocessing directive #pca
# pca 0 # Decompose a principal component subspace of
^
interfc.c:87:31: error: invalid preprocessing directive #the
# the data. Retain this many PCs. {default|0: all}
^
interfc.c:88:3: error: invalid preprocessing directive #Optional
# Optional input variables:
^
interfc.c:90:4: error: invalid preprocessing directive #WeightsInFile
# WeightsInFile input.wts # Starting ICA weight matrix (nchans,ncomps)
^
interfc.c:91:31: error: invalid preprocessing directive #{
# {default: identity or sphering matrix}
^
interfc.c:92:28: error: stray ‘#’ in program
lrate 2.0e-3 # Initial ICA learning rate (float << 1)
^
interfc.c:93:31: error: invalid preprocessing directive #{
# {default: heuristic ~5e-4}
^
interfc.c:94:5: error: invalid preprocessing directive #blocksize
# blocksize 20 # ICA block size (integer << datalength)
^
interfc.c:95:31: error: invalid preprocessing directive #{
# {default: heuristic fraction of log data length}
^
interfc.c:96:5: error: invalid preprocessing directive #stop
# stop 1.0e-6 # Stop training when weight-change < this value
^
interfc.c:97:31: error: invalid preprocessing directive #{
# {default: heuristic ~0.000001}
^
interfc.c:98:28: error: stray ‘#’ in program
maxsteps 512 # Max. number of ICA training steps {default: 128}
^
interfc.c:99:5: error: invalid preprocessing directive #posact
# posact on # Make each component activation net-positive
^
interfc.c:100:30: error: invalid preprocessing directive #(
# (on/off) {default: on}
^
interfc.c:101:5: error: invalid preprocessing directive #annealstep
# annealstep 0.98 # Annealing factor (range (0,1]) - controls
^
interfc.c:102:31: error: invalid preprocessing directive #the
# the speed of convergence.
^
interfc.c:103:5: error: invalid preprocessing directive #annealdeg
# annealdeg 60 # Angledelta threshold for annealing {default: 60}
^
interfc.c:104:5: error: invalid preprocessing directive #momentum
# momentum 0.0 # Momentum gain (range [0,1]) {default: 0}
^
interfc.c:105:5: error: invalid preprocessing directive #verbose
# verbose off # Give ascii messages (on/off) {default: on}
^
interfc.c:107:3: error: invalid preprocessing directive #Optional
# Optional outputs:
^
interfc.c:109:4: error: invalid preprocessing directive #ActivationsFile
# ActivationsFile data.act # Activations of each component (ncomps,points)
^
interfc.c:110:4: error: invalid preprocessing directive #BiasFile
# BiasFile data.bs # Bias weights (ncomps,1)
^
interfc.c:111:4: error: invalid preprocessing directive #SignFile
# SignFile data.sgn # Signs designating (-1) sub- and (1) super-Gaussian
^
interfc.c:112:31: error: invalid preprocessing directive #components
# components (ncomps,1)
^
interfc.c:114:3: error: invalid preprocessing directive #This
# This script, \"ica.sc\" is a sample ica script file. Copy and modify it as
^
interfc.c:114:17: warning: missing terminating " character
# This script, \"ica.sc\" is a sample ica script file. Copy and modify it as
^
interfc.c:115:3: error: invalid preprocessing directive #desired
# desired. Note that the input data file(s) must be native floats."
^
interfc.c:115:67: warning: missing terminating " character
# desired. Note that the input data file(s) must be native floats."
^
interfc.c: In function ‘help’:
interfc.c:170:3: error: missing terminating " character
puts(HELPMSG);
^
interfc.c:170:3: error: too few arguments to function ‘puts’
interfc.c: In function ‘doit’:
interfc.c:679:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘integer {aka long int}’ [-Wformat=]
printf("PDF will be calculated initially every %d blocks using %d data points.\n",extblocks,pdfsize);
^
interfc.c:679:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘integer {aka long int}’ [-Wformat=]
interfc.c:681:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘integer {aka long int}’ [-Wformat=]
printf("PDF will not be calculated. Exactly %d sub-Gaussian components assumed.\n",nsub);
^
interfc.c:684:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘integer {aka long int}’ [-Wformat=]
printf("Initial learning rate will be %g, block size %d.\n",lrate,block);
^
interfc.c:690:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘integer {aka long int}’ [-Wformat=]
printf("Training will end when wchange < %g or after %d steps.\n",nochange,maxsteps);
^
interfc.c: In function ‘master’:
interfc.c:923:16: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
keys->token = strdup(token);
^
Makefile:19: recipe for target 'interfc.o' failed
make: *** [interfc.o] Error 1
```
Любая помощь и намеки на то, что я могу сделать неправильно, будет принята с благодарностью!
Спасибо, Алекс