Problems compiling on CentOS 7.x

Hi All,

I’m having problems getting ANFI to compile on CentOS 7.

Firstly my reasons for compiling, we run a cluster using the “modules” system that allows us to have several versions of the same package available and dynamically switch between them. This requires of course installing in a non standard location.

As far as I know I have the packages required to compile installed and have generated a Makefile based on Makefile.linux_xorg7_64.

However when I try and compile after building a whole bunch of stuff it errors out with the following error…

if [ -f SUMA/SurfMesh ]; then /bin/cp -f SUMA/SurfMesh ./linux_xorg7_64 ; fi; \
/bin/cp -f scripts_install/@SUMA_* ./linux_xorg7_64 ;)
( cd ptaylor ;	\
./@MakeLocalMake	;\
make afni_install  ;	\
cd ../	;		)
Got relative path, append
Moved old Makefile to Makefile.back.2017.04.11
Local Makefile created.
make[1]: Entering directory `/storage/stsxab/CentosBuild/AFNI/afni_src/ptaylor'
Installing Binaries...
make[1]: Leaving directory `/storage/stsxab/CentosBuild/AFNI/afni_src/ptaylor'
( cd pkundu ;	\
./@install_pkundu ./linux_xorg7_64	;\
cd ../	;		)
Have relative path, turn to full
Coping to /storage/stsxab/CentosBuild/AFNI/afni_src/linux_xorg7_64
Copying meica.libs to /storage/stsxab/CentosBuild/AFNI/afni_src/linux_xorg7_64
/bin/cp -f -r jzosky/ jzosky/lib_RetroTS ./linux_xorg7_64
/bin/cp -f scripts_install/* ./linux_xorg7_64
/bin/mv -f afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3daxialize cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket 3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna 2dImReg 3dmaskave 3dbuc2fim byteorder imstack 3dDeconvolve 3dTcat 3drotate 3dvolreg 3dpc 3dfractionize 1dplot adwarp imupsam 3dIntracranial 24swap 3dTsmooth RSFgen float_scan 1dtranspose 3dFourier 3dNotes 3dROIstats 1deval 3dStatClust 3dTstat 3dmaskdump 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dnorm afni_vcheck 3ddot 3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign 3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid 3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum 3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow 3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval 3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI 3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat 3dThreetoRGB Ifile 3dresample 3dAutobox 3dLRflip 3dANALYZEtoAFNI dicom_hdr 3dDespike dicom_to_raw file_tool rotcom 1ddot 1dsvd 3dDeconvolve_f 3dAnhist 3dAFNIto3D 3dUniformize 3dWarp nicat 3dSpatNorm fftest serial_helper 3dDTeig 3dDWItoDT 3dWarpDrive nifti_tool 3dAllineate nifti1_test whereami plugout_drive 3dLSS 3dMedianFilter 3dretroicor 3dAFNItoNIML 3dAFNItoRaw im2niml 3dedge3 DTIStudioFibertoSegments Dimon1 Dimon 3dLocalstat 3danisosmooth 3dmaxima GLTsymtest 3dPval stimband 1dNLfit 3dTwotoComplex 3dInvFMRI 3dmatcalc 3dAcost 3dLocalBistat 3dFWHMx 3dBlurToFWHM 1dSEM 3dDFT 3dSynthesize 1dMarry 3dEmpty 3dsvm 1dFlagMotion 3dTsort 1dTsort 3dTfitter afni_history 1dUpsample 3dLocalSVD  niml_feedme  3dErrtsCormat 3dUndump 3dREMLfit 3dTnorm 3dUpsample 3dTcorrMap 3dmatmult 3dABoverlap 3dmaskSVD 1dBandpass 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip 3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D 3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply 1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport 3dNormalityTest 3dmask_tool FIRdesign help_format 2perm 3dClustCount column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog 3dNwarpAdjust 3dNwarpFuncs 3dTproject afni_open 3dConformist 3dNwarpXYZ 3dTRfix 3dToyProg 3dRankizer nifti1_tool gifti_tool cifti_tool images_equal uniq_images tokens 3dLocalACF 3dXClustSim 3dtoXdataset 3dMultiThresh 3dLFCD 3dDegreeCentrality 3dECM 3dMSE 3dsvm_linpredict 3dTfilter 3dTsplit4D 3dSharpen 3dExtractGroupInCorr cjpeg djpeg whirlgif mpeg_encode myget Xphace rmz aiv mycat quotize balloon ./linux_xorg7_64
/bin/mv: cannot stat ‘cjpeg’: No such file or directory
/bin/mv: cannot stat ‘djpeg’: No such file or directory
make: *** [install] Error 1

I can post the Makefile if that would help, and / or a complete log.

Does anyone know what the problem is or how to fix it.



Hi Phill,

There is nothing there that suggests what went wrong,
however you might consider starting with a more current
Makefile, such as other_builds/Makefile.linux_fedora_19_64.
We do not currently have such a build system to test with,
though maybe we could try on at RH 6 one…

Are you running bash or tcsh? Assuming bash, please run
the following commands:

cd afni_src
cp other_builds/Makefile.linux_fedora_19_64 Makefile
make cleanest
make itall 2>&1 | tee out.make.f19.txt

And mail me that output text file (reynoldr .AT.


  • rick

Thanks Rick,

Using that Makefile and modifying so it could find my GSL include & biaries has worked, well it got all the way through without errors.

Now I presume I just move the contents of the linux_fedora_19_64 folder to where I want them and set my paths and AFNI_PLUGINPATH to point to them.



That is good news, thanks.

And you are right about putting it wherever you want to.

Note that the Makefile has a top-level SYSTEM_NAME variable,
which then propagates to INSTALLDIR, which is the name of
the output directory. You could certainly modify them as you
see fit.

  • rick