This GLIBCXX error appears when running our Centos 6 build on an older OS. Try using our Centos 4 build.
Nick On Mon, 2014-02-17 at 09:32 -0500, Bruce Fischl wrote: > yes, it certainly looks like a library problem. You should talk to your > sysadmin, or perhaps Zeke or Nick can comment > > cheers > Bruce > On Mon, 17 Feb 2014, Durai > Arasan wrote: > > > Hi Freesurfer experts, > > so I got this error when I ran recon-all on my cluster. I am really hoping > > this is just a case of missing GCC libraries and nothing is wrong with the > > Freesurfer installation on the nodes. Kindly confirm this. > > > > Thank you > > > > *************************************************************************** > > ******************************************************* > > > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > INFO: SUBJECTS_DIR is /****************** > > Actual FREESURFER_HOME /************************************** > > Linux ***************************** SMP Fri Mar 22 05:41:51 EDT 2013 x86_64 > > x86_64 x86_64 GNU/Linux > > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_convert) > > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_convert) > > mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_convert) > > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_convert) > > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_convert) > > mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_convert) > > tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by tkregister2_cmdl) > > tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by tkregister2_cmdl) > > tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by tkregister2_cmdl) > > mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_make_uchar) > > mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_make_uchar) > > mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_make_uchar) > > mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_normalize) > > mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_normalize) > > mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_normalize) > > mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_watershed) > > mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_watershed) > > mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_watershed) > > mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_gcut) > > mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_gcut) > > mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_gcut) > > mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_segment) > > mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_segment) > > mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_segment) > > mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_label2label) > > mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mri_label2label) > > mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by mri_label2label) > > mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_em_register) > > mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mri_em_register) > > mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by mri_em_register) > > mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_ca_normalize) > > mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mri_ca_normalize) > > mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by mri_ca_normalize) > > mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_ca_register) > > mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mri_ca_register) > > mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by mri_ca_register) > > mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_ca_label) > > mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_ca_label) > > mri_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_ca_label) > > mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_pretess) > > mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_pretess) > > mri_pretess: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_pretess) > > mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_fill) > > mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_fill) > > mri_fill: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_fill) > > mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_tessellate) > > mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_tessellate) > > mri_tessellate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_tessellate) > > mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_concatenate_lta) > > mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mri_concatenate_lta) > > mri_concatenate_lta: /lib64/libc.so.6: version `GLIBC_2.7' not found > > (required by mri_concatenate_lta) > > mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_normalize_tp2) > > mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mri_normalize_tp2) > > mri_normalize_tp2: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by mri_normalize_tp2) > > mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mris_smooth) > > mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mris_smooth) > > mris_smooth: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mris_smooth) > > mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mris_inflate) > > mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mris_inflate) > > mris_inflate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mris_inflate) > > mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mris_curvature) > > mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mris_curvature) > > mris_curvature: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mris_curvature) > > mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mris_sphere) > > mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mris_sphere) > > mris_sphere: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mris_sphere) > > mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mris_fix_topology) > > mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mris_fix_topology) > > mris_fix_topology: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by mris_fix_topology) > > mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mris_topo_fixer) > > mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mris_topo_fixer) > > mris_topo_fixer: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by mris_topo_fixer) > > mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mris_ca_label) > > mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mris_ca_label) > > mris_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mris_ca_label) > > mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mris_euler_number) > > mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mris_euler_number) > > mris_euler_number: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > > by mris_euler_number) > > mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mris_make_surfaces) > > mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mris_make_surfaces) > > mris_make_surfaces: /lib64/libc.so.6: version `GLIBC_2.7' not found > > (required by mris_make_surfaces) > > mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mris_register) > > mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mris_register) > > mris_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mris_register) > > mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mris_volmask) > > mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mris_volmask) > > mris_volmask: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mris_volmask) > > mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > > not found (required by mris_anatomical_stats) > > mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' > > not found (required by mris_anatomical_stats) > > mris_anatomical_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found > > (required by mris_anatomical_stats) > > mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mrisp_paint) > > mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mrisp_paint) > > mrisp_paint: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mrisp_paint) > > mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > > not found (required by mris_curvature_stats) > > mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mris_curvature_stats) > > mris_curvature_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found > > (required by mris_curvature_stats) > > mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mris_calc) > > mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mris_calc) > > mris_calc: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mris_calc) > > mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_robust_register) > > mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mri_robust_register) > > mri_robust_register: /lib64/libc.so.6: version `GLIBC_2.7' not found > > (required by mri_robust_register) > > mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > > found (required by mri_robust_template) > > mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > > found (required by mri_robust_template) > > mri_robust_template: /lib64/libc.so.6: version `GLIBC_2.7' not found > > (required by mri_robust_template) > > mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_and) > > mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_and) > > mri_and: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_and) > > mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_or) > > mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_or) > > mri_or: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_or) > > mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > > not found (required by mri_fuse_segmentations) > > mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' > > not found (required by mri_fuse_segmentations) > > mri_fuse_segmentations: /lib64/libc.so.6: version `GLIBC_2.7' not found > > (required by mri_fuse_segmentations) > > mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_segstats) > > mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_segstats) > > mri_segstats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_segstats) > > /****************/***444 > > > > mri_convert /********************/***_mp.nii > > /*******************/****444/mri/orig/001.mgz > > > > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_convert) > > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_convert) > > mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_convert) > > Linux ************************************ ************************ SMP Fri > > Mar 22 ******** EDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s ***444 exited with ERRORS at Mon Feb 17 02:24:00 EST 2014 > > > > For more details, see the log file > > **********************/***444/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > _______________________________________________ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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