mrirecon
Compile fail on CentOS
I am trying to compile BART 0.5.00 on a CentOS cluster. I cloned the master branch from git, and encountered the following error:
gcc -Wall -Wextra -MMD -MF /var/scratch/tbbakker/bart/src/num/.lapack.d -iquote /var/scratch/tbbakker/bart/src/ -I/usr//include/ -I/usr//include -DFFTWTHREADS -DMAIN_LIST="avg, bench, bitmask, cabs, caldir, calmat, carg, casorati, cc, ccapply, cdf97, circshift, conj, conv, copy, cpyphs, creal, crop, delta, ecalib, ecaltwo, estdelay, estdims, estshift, estvar, extract, fakeksp, fft, fftmod, fftrot, fftshift, filter, flatten, flip, fmac, homodyne, index, invert, itsense, join, looklocker, lrmatrix, mandelbrot, mip, moba, nlinv, noise, normalize, nrmse, nufft, ones, pattern, phantom, pics, pocsense, poisson, poly, repmat, reshape, resize, rmfreq, rof, rss, sake, saxpy, scale, sdot, show, slice, spow, sqpics, squeeze, ssa, std, svd, tgv, threshold, toimg, traj, transpose, twixread, var, vec, version, walsh, wave, wavelet, wavepsf, whiten, window, wshfl, zeros, zexp, ()" -include src/main.h -O3 -ffast-math -Wmissing-prototypes -std=gnu11 -fopenmp -c -o /var/scratch/tbbakker/bart/src/num/lapack.o /var/scratch/tbbakker/bart/src/num/lapack.c /var/scratch/tbbakker/bart/src/num/lapack.c:14:21: fatal error: lapacke.h: No such file or directory #include <lapacke.h> ^ compilation terminated. make[1]: *** [/var/scratch/tbbakker/bart/src/num/lapack.o] Error 1
I don't have root access on this system, so could not follow the instructions detailed in the README for installation on CentOS:
sudo yum install devtoolset-8 atlas-devel fftw3-devel libpng-devel lapack-devel
Instead, given the error, I tried building lapack (version 3.9.0) from source. Unfortunately, the error remains.
I tried inspecting the Makefile for a hint, and found the following lines:
ifeq ($(BUILDTYPE), Linux) ifneq (,$(findstring Red Hat,$(shell gcc --version))) CPPFLAGS+=-I/usr/include/lapacke/ LDFLAGS+=-L/usr/lib64/atlas -laterals endif endif
I suspect this tells the compiler where to look for the missing lapacke.h? As a side-note, this line was missing from the Makefile in bart-0.5.00.tar I obtained from the BART webpage in another attempt to solve this issue (is this intentional?).
Regardless, /usr/include/lapacke/ indeed exists on this system, and contains (among other files) a file lapacke.h. I'm rather unfamiliar with these systems, and am unsure how to proceed.
CentOS version: CentOS Linux release 7.4.1708 (Core) BART version: 0.5.00
Thanks for the quick reply!
That definitely did something, I now get the following error:
gcc -rdynamic -O3 -ffast-math -Wmissing-prototypes -std=gnu11 -fopenmp -Wall -Wextra -DNOLAPACKE -MMD -MF ./.bart.d -iquote /var/scratch/t bbakker/bart/src/ -Isrc/lapacke -I/usr//include/ -I/usr//include -DFFTWTHREADS -DMAIN_LIST="avg, bench, bitmask, cabs, caldir, calmat, car g, casorati, cc, ccapply, cdf97, circshift, conj, conv, copy, cpyphs, creal, crop, delta, ecalib, ecaltwo, estdelay, estdims, estshift, es tvar, extract, fakeksp, fft, fftmod, fftrot, fftshift, filter, flatten, flip, fmac, homodyne, index, invert, itsense, join, looklocker, lr matrix, mandelbrot, mip, moba, nlinv, noise, normalize, nrmse, nufft, ones, pattern, phantom, pics, pocsense, poisson, poly, repmat, resha pe, resize, rmfreq, rof, rss, sake, saxpy, scale, sdot, show, slice, spow, sqpics, squeeze, ssa, std, svd, tgv, threshold, toimg, traj, tr anspose, twixread, var, vec, version, walsh, wave, wavelet, wavepsf, whiten, window, wshfl, zeros, zexp, ()" -include src/main.h -Dmain_re al=main_bart -o bart src/main.c /var/scratch/tbbakker/bart/src/bart.o lib/libbox.a lib/libgrecon.a lib/libsense.a lib/libnoir.a lib/libite r.a lib/liblinops.a lib/libwavelet.a lib/liblowrank.a lib/libnoncart.a lib/libcalib.a lib/libsimu.a lib/libsake.a lib/libdfwavelet.a lib/l ibnlops.a lib/libmoba.a lib/libnum.a lib/libmisc.a lib/libnum.a lib/libmisc.a lib/liblapacke.a -L/usr//lib -lfftw3f -lfftw3f_threads -L/u sr//lib -llapack -lblas -lpng -lm
/cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libm.so when searching for -lm /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libm.so when searching for -lm /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libgcc_s.so.1 when searching for libgcc_s.so.1 /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libgcc_s.so.1 when searching for libgcc_s.so.1 /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libpthread.so when searching for -lpthread /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libpthread.so when searching for -lpthread /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libc.so when searching for -lc /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libc.so when searching for -lc /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libgcc_s.so.1 when searching for libgcc_s.so.1 /cm/shared/package/gcc/4.9.2/bin/ld: skipping incompatible /usr//lib/libgcc_s.so.1 when searching for libgcc_s.so.1
lib/libnum.a(blas.o): In function `blas_cgemm': blas.c:(.text+0x7e): undefined reference to `cblas_cgemm' lib/libnum.a(blas.o): In function `blas_matrix_multiply': blas.c:(.text+0xf7): undefined reference to `cblas_cgemm' lib/libnum.a(blas.o): In function `blas_csyrk': blas.c:(.text+0x18c): undefined reference to `cblas_csyrk' collect2: error: ld returned 1 exit status make[1]: *** [bart] Error 1
Followed by a bunch of Field 'name' not cached: and Field 'hname' not cached:.
There are packages for CentOS 8. Does this help?
https://copr.fedorainfracloud.org/coprs/schaten/bart/