Bug 2046933
Summary: | quantum-espresso: FTBFS in Fedora rawhide/f36 | ||||||||||
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Product: | [Fedora] Fedora | Reporter: | Fedora Release Engineering <releng> | ||||||||
Component: | quantum-espresso | Assignee: | marcindulak <Marcin.Dulak> | ||||||||
Status: | CLOSED RAWHIDE | QA Contact: | Fedora Extras Quality Assurance <extras-qa> | ||||||||
Severity: | unspecified | Docs Contact: | |||||||||
Priority: | unspecified | ||||||||||
Version: | rawhide | CC: | Marcin.Dulak | ||||||||
Target Milestone: | --- | ||||||||||
Target Release: | --- | ||||||||||
Hardware: | Unspecified | ||||||||||
OS: | Unspecified | ||||||||||
Whiteboard: | |||||||||||
Fixed In Version: | Doc Type: | If docs needed, set a value | |||||||||
Doc Text: | Story Points: | --- | |||||||||
Clone Of: | Environment: | ||||||||||
Last Closed: | 2022-01-30 15:53:13 UTC | Type: | --- | ||||||||
Regression: | --- | Mount Type: | --- | ||||||||
Documentation: | --- | CRM: | |||||||||
Verified Versions: | Category: | --- | |||||||||
oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |||||||||
Cloudforms Team: | --- | Target Upstream Version: | |||||||||
Embargoed: | |||||||||||
Bug Depends On: | |||||||||||
Bug Blocks: | 1992484 | ||||||||||
Attachments: |
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Description
Fedora Release Engineering
2022-01-27 09:43:22 UTC
Created attachment 1856417 [details]
build.log
file build.log too big, will only attach last 32768 bytes
Created attachment 1856418 [details]
root.log
file root.log too big, will only attach last 32768 bytes
Created attachment 1856419 [details]
state.log
Currently all tests (All done. ERROR: only 0 out of 226 tests passed (1 skipped).) on f36 x86_64, gfortran-12 fail with "Program received signal SIGSEGV: Segmentation fault - invalid memory reference". It seems like the failures can be associated with the "-flto=auto" option. Appending the "-fno-lto" option can be used as a workaround to make most of the tests (220 out of 226, depending on mpi used) pass on f36 x86_64. The test failures can be reproduced using the following Dockerfile ``` FROM fedora:36@sha256:dfb26a5dbc30de897f86e60870a4b4000c7733545e866fd1c03637a931b2d4e3 # Install packaging tools RUN dnf install -y \ git fedpkg fedora-packager curl # Install build dependencies RUN dnf install -y \ make python3 python3-numpy python numpy gcc-gfortran flexiblas-devel flexiblas-openblas-serial openblas-serial fftw3-devel \ openssh-clients openmpi-devel scalapack-openmpi-devel mpich-devel scalapack-mpich-devel which RUN mkdir -p /root/espresso/pseudo/ \ && curl -Lo /root/espresso/pseudo/Si.pz-vbc.UPF http://nninc.cnf.cornell.edu/psp_files/Si.pz-vbc.UPF CMD ["/bin/bash"] ``` Build the image and enter the container ``` docker build -t qe:latest . docker run -it --rm --name qe qe:latest ``` Compile and run tests ``` mkdir /qe && cd /qe curl -LO https://github.com/QEF/q-e/archive/refs/tags/qe-7.0.tar.gz tar zxf qe-7.0.tar.gz && cd q-e-qe-7.0 sed -i 's|FOX_FLAGS = @foxflags@|FOX_FLAGS = $(FOXFLAGS)|' install/make.inc.in module load mpi/openmpi-x86_64 export FLAGS='-fallow-argument-mismatch -O2 -flto=auto' make clean || true export FCFLAGS=$FLAGS && export CFLAGS=$FLAGS && export FFLAGS=$FLAGS && export FOXFLAGS="$FLAGS -fPIE -x f95-cpp-input" ./configure && make all cd test-suite/pw_pbe/ ../../bin/pw.x < pbe0-si111.in ``` Result: ``` Program PWSCF v.7.0 starts on 30Jan2022 at 9:26:43 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017); "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/quote Parallel version (MPI), running on 1 processors MPI processes distributed on 1 nodes 2023 MiB available memory on the printing compute node when the environment starts Waiting for input... Reading input from standard input Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 4 IMPORTANT: XC functional enforced from input : Exchange-correlation= PBE0 ( 6 4 8 4 0 0 0) EXX-fraction = 0.25 Any further DFT definition will be discarded Please, verify this is what you really want [b9f6c41c0f52:34998:0:34998] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil)) ==== backtrace (tid: 34998) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f6ea90faf14] 1 /lib64/libucs.so.0(+0x2865d) [0x7f6ea90fb65d] 2 /lib64/libucs.so.0(+0x28845) [0x7f6ea90fb845] 3 ../../bin/pw.x() [0x878e92] 4 ../../bin/pw.x() [0x87bd7a] 5 ../../bin/pw.x() [0x528976] 6 ../../bin/pw.x() [0x588ebf] 7 ../../bin/pw.x() [0x40889f] 8 ../../bin/pw.x() [0x407bad] 9 /lib64/libc.so.6(+0x2d590) [0x7f6eaee3a590] 10 /lib64/libc.so.6(__libc_start_main+0x89) [0x7f6eaee3a649] 11 ../../bin/pw.x() [0x407bd5] ================================= Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x7f6eaf178a32 in ??? #1 0x7f6eaf177bc5 in ??? #2 0x7f6eaee4fadf in ??? #3 0x878e92 in ??? at ../../Modules/qes_init_module.f90:2340 #4 0x87bd79 in pw_init_qexsd_input_.constprop.0 at /qe/q-e-qe-7.0/PW/src/pw_init_qexsd_input.f90:475 #5 0x528975 in iosys_ at /qe/q-e-qe-7.0/PW/src/input.f90:1729 #6 0x588ebe in run_pwscf_ at /qe/q-e-qe-7.0/PW/src/run_pwscf.f90:102 #7 0x40889e in pwscf at /qe/q-e-qe-7.0/PW/src/pwscf.f90:85 #8 0x407bac in main at /qe/q-e-qe-7.0/PW/src/pwscf.f90:40 Segmentation fault (core dumped) ``` Example build which uses "-flto=auto" with test segmentation faults https://koji.fedoraproject.org/koji/taskinfo?taskID=82138626 Example build with appended "-fno-lto" with most tests passing https://koji.fedoraproject.org/koji/taskinfo?taskID=82138836 Reported upstream https://gitlab.com/QEF/q-e/-/issues/460 Built using -fno-lto workaround in https://koji.fedoraproject.org/koji/taskinfo?taskID=82142229 |