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Upgrade cannot execute binary file: Exec format error

Discussion in 'Install & Upgrades or Pre-Install Questions' started by KlueMaster, Dec 9, 2025.

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  1. Dec 9, 2025 #1
    KlueMaster

    KlueMaster Member

    78
    11
    8
    Aug 5, 2017
    Ratings:
    +32
    Local Time:
    9:34 AM
    MariaDB 10
    Getting errors as:
    Code (Text):
    /usr/local/src/centminmod/inc/memcheck.inc: line 29: /bin/expr: cannot execute binary file: Exec format error
/usr/local/src/centminmod/inc/memcheck.inc: line 29: /bin/expr: cannot execute binary file: Exec format error

/usr/local/src/centminmod/inc/cpcheck.inc: line 161: /bin/iconv: cannot execute binary file: Exec format error
/usr/local/src/centminmod/inc/cpcheck.inc: line 161: /bin/iconv: cannot execute binary file: Exec format error

    • CentOS Version: AlmaLinux 9
    • Centmin Mod Version Installed: 132.00stable
    • Nginx Version Installed: 1.29.2
    • PHP Version Installed: 8.3.15
    • MariaDB MySQL Version Installed: 10.6.23
    • When was last time updated Centmin Mod code base ? : just now
    • Persistent Config:
      Code (Text):
      LETSENCRYPT_DETECT='y'
PHPFINFO=y

MARCH_TARGETNATIVE='n'

SET_DEFAULT_MYSQLCHARSET='utf8mb4'
SELFSIGNEDSSL_ECDSA='y'
PHPFINFO='y'
PHP_OVERWRITECONF='n'
PYTHON_INSTALL_ALTERNATIVES='y'

     
  2. Dec 10, 2025 #2
    eva2000

    eva2000 Administrator Staff Member

    58,893
    12,490
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +19,122
    Local Time:
    2:04 PM
    Nginx 1.31.x
    MariaDB 10.x/11.4+/12.3+
    Did you recently change servers while on VPS? were both VPS servers using same cpu architecture ? Or web host moving your VPS instance from one VPS host node to another?

    what is output for commands
    Code (Text):
    uname -m

    Code (Text):
    file /bin/expr /bin/iconv

    rpm -v should return empty if ok
    Code (Text):
    rpm -V coreutils glibc-common

    Code (Text):
    yum -q history list coreutils glibc-common


    example for
    Code (Text):
    uname -m
x86_64

file /bin/expr /bin/iconv
/bin/expr:  ELF 64-bit LSB pie executable, x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, BuildID[sha1]=f096da8553259b5b13e4addb27b061df87bd9f77, for GNU/Linux 3.2.0, stripped
/bin/iconv: ELF 64-bit LSB pie executable, x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, BuildID[sha1]=dd72341337a7f76f6f93f5bb6b85e1ac6a35baaf, for GNU/Linux 3.2.0, stripped
     
  3. Dec 10, 2025 #3
    KlueMaster

    KlueMaster Member

    78
    11
    8
    Aug 5, 2017
    Ratings:
    +32
    Local Time:
    9:34 AM
    MariaDB 10
    No move happened at all. I'm on the same server for years, although had migrated from CentOS to AlmaLinux in the beginning of this year. The issue happened after recent cmupdate.

    Code (Text):
    # uname -m
x86_64

# file /bin/expr /bin/iconv
/bin/expr:  data
/bin/iconv: data

# rpm -V coreutils glibc-common
..5......    /usr/bin/base32
..5......    /usr/bin/basenc
..5......    /usr/bin/chcon
..5......    /usr/bin/chgrp
..5......    /usr/bin/cksum
..5......    /usr/bin/comm
..5......    /usr/bin/csplit
..5......    /usr/bin/dir
..5......    /usr/bin/du
..5......    /usr/bin/expand
..5......    /usr/bin/expr
..5......    /usr/bin/factor
..5......    /usr/bin/false
..5......    /usr/bin/fmt
..5......    /usr/bin/fold
..5......    /usr/bin/groups
..5......    /usr/bin/hostid
..5......    /usr/bin/install
..5......    /usr/bin/join
..5......    /usr/bin/link
..5......    /usr/bin/logname
..5......    /usr/bin/md5sum
..5......    /usr/bin/nl
..5......    /usr/bin/nohup
..5......    /usr/bin/numfmt
..5......    /usr/bin/od
..5......    /usr/bin/pr
..5......    /usr/bin/ptx
..5......    /usr/bin/tac
..5......    /usr/bin/unexpand
..5......    /usr/bin/unlink
..5......    /usr/bin/vdir
..5......    /usr/bin/who
..5......    /usr/bin/yes
missing   a /usr/lib/.build-id/00/0c0703951442b344a82fca6f6ba1e06fac5bd3 (Bad message)
missing   a /usr/lib/.build-id/00/8edd3985936f541dc2b92891746b6026c63f2f (Bad message)
missing   a /usr/lib/.build-id/00/f7cfe2c345bd8f8b532d41cfbbb9cc704d350e (Bad message)
missing   a /usr/lib/.build-id/05/799eef254e5d216b2ea08a12efbba7d4338020 (Bad message)
missing   a /usr/lib/.build-id/05/ddf0dfc9262d20f444d7821c428b09fe109b72 (Bad message)
missing   a /usr/lib/.build-id/10/a73314f0540b5fb701f2e72300b442140d9df7 (Bad message)
missing   a /usr/lib/.build-id/13/aee31a125a45df2c5842fa2eeb9c54d8027d82 (Bad message)
missing   a /usr/lib/.build-id/14/dc8c8645ce9eb19595474e1f5847d2f910cc80 (Bad message)
missing   a /usr/lib/.build-id/1b/761596862eb2812d3d704a5828aefd592b6c8a (Bad message)
missing   a /usr/lib/.build-id/1d/3668016858f4412892f8b3cf737ebe3a14286d (Bad message)
missing   a /usr/lib/.build-id/20/8046a55379dbd16743632edb6f9a41d79943e7 (Bad message)
missing   a /usr/lib/.build-id/21/5d223c8282b6787e65aed9bef550ece6da6d3c (Bad message)
missing   a /usr/lib/.build-id/21/8d5a39fe1ecf301c0405319e2a13b800f9d875 (Bad message)
missing   a /usr/lib/.build-id/22/a19c203191cf55bf1810fae6df4e36be34e9be (Bad message)
missing   a /usr/lib/.build-id/26/c04c811911d89ee6ba871e9da600defabbfd15 (Bad message)
missing   a /usr/lib/.build-id/27/324472b2393d80a7a07473dd35f2f237e249fd (Bad message)
missing   a /usr/lib/.build-id/27/e0c94d865d6c83d2491e11e5a6edbf14764345 (Bad message)
missing   a /usr/lib/.build-id/2a/de02f5b139e61bbb4b30c0dbc3a3467031534c (Bad message)
missing   a /usr/lib/.build-id/2c/52d3265fe4674f5792ac9dce7570971ac2ddda (Bad message)
missing   a /usr/lib/.build-id/2e/974e8b79fd897b67b9bf322dfd3e0b5aea3b48 (Bad message)
missing   a /usr/lib/.build-id/34/8a1d7475c63adebd8f8152c73fe03418924fba (Bad message)
missing   a /usr/lib/.build-id/35/aa243764d52ed610fdd7f19121cd2530600ea3 (Bad message)
missing   a /usr/lib/.build-id/35/f2b6c15557a795adbff037f3cfc3c6d4af0ec5 (Bad message)
missing   a /usr/lib/.build-id/39/6ed55d7fc69138bb34bc87213be5ec590fa860 (Bad message)
missing   a /usr/lib/.build-id/3b/8daff481ebd20e90e83520b65d0b329f28eee1 (Bad message)
missing   a /usr/lib/.build-id/3d/37884697775d9021dc23610499ebdf2b1e13ca (Bad message)
missing   a /usr/lib/.build-id/3d/432e0857a674812f17f9fad9103ecaa37e943a (Bad message)
missing   a /usr/lib/.build-id/3d/8c941db9ceb0bbccb59dd81d28cfa7d769704b (Bad message)
missing   a /usr/lib/.build-id/3e/cb4c20472b89af7545edfc9d2603314fba74d8 (Bad message)
missing   a /usr/lib/.build-id/40/2ae5bedd7837eb1b5f44575a7255f96c1f0ca9 (Bad message)
missing   a /usr/lib/.build-id/44/0d2c055659739cd43ad313ed3fcac8182560c2 (Bad message)
missing   a /usr/lib/.build-id/44/473158ab3e16581293d7307461093f3f2a19a1 (Bad message)
missing   a /usr/lib/.build-id/4c/3452b68b18e75db24e75b45d5d7d9e58ef3e31 (Bad message)
missing   a /usr/lib/.build-id/4d/61534451e8a3b2444ecb3e779c2eff61b93e1d (Bad message)
missing   a /usr/lib/.build-id/4d/d1999ef989562725e2ab404c83951b149778a3 (Bad message)
missing   a /usr/lib/.build-id/4f/fc65cb7ebc0903a56393860d36f7aac89015a5 (Bad message)
missing   a /usr/lib/.build-id/51/030978f22f8591d43094863552c967f9b452f1 (Bad message)
missing   a /usr/lib/.build-id/56/fd392853859cdeac370504415bab95270e61f6 (Bad message)
missing   a /usr/lib/.build-id/58/152ad09f49452ab7e4f9dbed7666118b5ed335 (Bad message)
missing   a /usr/lib/.build-id/58/232583e0f01a0b86a56e96734c75ea67ae4a8f (Bad message)
missing   a /usr/lib/.build-id/58/7206f4346b2452b58febc8057a3f2e18623690 (Bad message)
missing   a /usr/lib/.build-id/5b/941cd7cc7261d9a3ca5ebfc2c4fc18d2a3beeb (Bad message)
missing   a /usr/lib/.build-id/5c/9680fccbeaa01e228d810a9027815cfda6d387 (Bad message)
missing   a /usr/lib/.build-id/5e/0d2046032faecb4537983c3636023bf276f058 (Bad message)
missing   a /usr/lib/.build-id/61/0b161270c2f0e9a464e8d8d828ba27ec581624 (Bad message)
missing   a /usr/lib/.build-id/62/e4ac297289323322fc1679f597a12f381e70f5 (Bad message)
missing   a /usr/lib/.build-id/65/58521d92afbce05199437ec2e116f1ff493ed8 (Bad message)
missing   a /usr/lib/.build-id/67/b52e61680edb8a84f57dd823abd716c34d1f3e (Bad message)
missing   a /usr/lib/.build-id/6e/fe890f0502e29c4ccc88cf22e6cc54b13d8687 (Bad message)
missing   a /usr/lib/.build-id/6f/7dcac054c6fe7f4dc434608ba2dd6fcd930406 (Bad message)
missing   a /usr/lib/.build-id/75/558b2311820cd2182a782ff8ebe66b2fab5908 (Bad message)
missing   a /usr/lib/.build-id/76/65ac0a40ea1243f9001fc16768381360750028 (Bad message)
missing   a /usr/lib/.build-id/76/8b04b9d9fd8e917793446a42cab3f319c82e73 (Bad message)
missing   a /usr/lib/.build-id/77/3c4deef7f3ff55b8000b1d23460d9001106d00 (Bad message)
missing   a /usr/lib/.build-id/7b/c2c1812bac1eb750d49e3ecd115d77f2ad1109 (Bad message)
missing   a /usr/lib/.build-id/7e/199cad1cbfc703d3b0f71ae212f61e812912e9 (Bad message)
missing   a /usr/lib/.build-id/7f/59b0124f85d05ef8828e6ac67cec5ec76a6b64 (Bad message)
missing   a /usr/lib/.build-id/7f/aed0146975e3faf36fc51202f5a3765c21050e (Bad message)
missing   a /usr/lib/.build-id/82/6360bad5c1747e9789b83f75776281ec8c77e5 (Bad message)
missing   a /usr/lib/.build-id/88/5e44a00da5989080fda19c8400e416e1f5046a (Bad message)
missing   a /usr/lib/.build-id/8a/6274506f181e5fb720125e934428bed7db2135 (Bad message)
missing   a /usr/lib/.build-id/8a/85992ade2eceb74b30324cdf32cb4677421765 (Bad message)
missing   a /usr/lib/.build-id/8e/b3b9a651a3bfb3a4dc60eeb6975c3c9f177529 (Bad message)
missing   a /usr/lib/.build-id/92/403f1f8985f6dba0ea62bf1d74c434537cc970 (Bad message)
missing   a /usr/lib/.build-id/94/c36bc4246fc52291c296f216863a4b17f88b2b (Bad message)
missing   a /usr/lib/.build-id/a1/20dcaed40826ed36a3eac448b061608cbdf815 (Bad message)
missing   a /usr/lib/.build-id/a2/533b5ee76d7eb1ee7695371508144e0373ec1e (Bad message)
missing   a /usr/lib/.build-id/a9/4a2acf861bfc100b5ff828c05bcd295bf527a2 (Bad message)
missing   a /usr/lib/.build-id/a9/97cc605c0e0877c43f5ccf3dc98de46d36138e (Bad message)
missing   a /usr/lib/.build-id/ae/22f7853319629b78875cd8f294ec8f25f5e043 (Bad message)
missing   a /usr/lib/.build-id/b0/a4edc35ced15ded9d4a6a7227973dd22219655 (Bad message)
missing   a /usr/lib/.build-id/b6/8916cf76c7240187716da2d7a36b64a9e1769c (Bad message)
missing   a /usr/lib/.build-id/b8/61237d2e16e8131521d46043678cd27322c651 (Bad message)
missing   a /usr/lib/.build-id/be/788675014d457f7ad2ae38fce2c2ebe685a333 (Bad message)
missing   a /usr/lib/.build-id/bf/6495c909c36f73adcbcc4e054303b85b8916cd (Bad message)
missing   a /usr/lib/.build-id/bf/78fb08acfad2103b748fcbc3f269d68036bf00 (Bad message)
missing   a /usr/lib/.build-id/c0/10ef04b0bd7816b1c0263de9922b818f4bfb96 (Bad message)
missing   a /usr/lib/.build-id/c1/af9f415e2becc38cae1aa41fb734ac636acc37 (Bad message)
missing   a /usr/lib/.build-id/c7/75b19023fb857b767cd6075af76a8b592fe026 (Bad message)
missing   a /usr/lib/.build-id/cc/a09691e9cda4e1169d65324cf2dd59fb790ec4 (Bad message)
missing   a /usr/lib/.build-id/cd/842227f32dc30d12c73f384ae2b0f4669c5420 (Bad message)
missing   a /usr/lib/.build-id/d8/59f4cd823e1b22a55ce62bccfcfa8ff3b58c54 (Bad message)
missing   a /usr/lib/.build-id/dc/760696fd18ecb92716e3f5fd29fe84caa2bcf7 (Bad message)
missing   a /usr/lib/.build-id/e2/c4268edecf7889f824a35c978f98df41a44906 (Bad message)
missing   a /usr/lib/.build-id/e5/d082ae7966ff40826b13f5e5def4b32c47d68c (Bad message)
missing   a /usr/lib/.build-id/e8/391c18d09913426be42be51b65d8b0fff469af (Bad message)
missing   a /usr/lib/.build-id/eb/89f3719bc534f686437cc911c3b2409ded4c5b (Bad message)
missing   a /usr/lib/.build-id/ed/716b7bf4a434615ced9b0082340dbaa03c392f (Bad message)
missing   a /usr/lib/.build-id/f0/96da8553259b5b13e4addb27b061df87bd9f77 (Bad message)
missing   a /usr/lib/.build-id/f4/1cbe79d5ba0c77e8f4ccadf660b67bc571e1e3 (Bad message)
missing   a /usr/lib/.build-id/f8/b8c9d8bf1b890a1e9e837c5709245516611fe0 (Bad message)
missing   a /usr/lib/.build-id/fa/fe60771ac75ab6a36d585dd067d281f874f394 (Bad message)
missing   a /usr/lib/.build-id/fd/ded6996a2114ead0882fde95b52598b5388bb9 (Bad message)
missing     /usr/libexec/coreutils/libstdbuf.so (Bad message)
..5......    /usr/bin/iconv
..5......    /usr/bin/localedef
missing   a /usr/lib/.build-id/03/f500eaede1140c2cd417bb1cf64fe9e4c921ff (Bad message)
missing   a /usr/lib/.build-id/37/832cedce53bdef49f84466f88e715e27d118e7 (Bad message)
missing   a /usr/lib/.build-id/5b/8069e0cea772924592c39b1787864806e1d1bb (Bad message)
missing   a /usr/lib/.build-id/84/97808af3fb6a0d4951c186520e0a6522934549 (Bad message)
missing   a /usr/lib/.build-id/d5/c8c0fda602b3e9d9b86dfd8a26ff4207841592 (Bad message)
missing   a /usr/lib/.build-id/d9/95fe822fbc6c279f39a5a3b68d7f7e13aa877d (Bad message)
missing   a /usr/lib/.build-id/da/cdb507e9afdadb9cf2ff671435fcfbbd7095cb.3 (Bad message)
missing   a /usr/lib/.build-id/f3/1eebadffee7945b5484cb15cf65124abd4d9c1 (Bad message)
missing   a /usr/lib/.build-id/fd/6c65a182fadc10db326af0bdf7ec5203128951 (Bad message)
..5......    /usr/lib/locale/C.utf8/LC_CTYPE
missing     /usr/lib/locale/C.utf8/LC_MESSAGES/SYS_LC_MESSAGES (Bad message)

ID     | Command line                                                                                                               | Date and time    | Action(s)      | Altered
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
    72 | update --disableplugin=priorities --setopt=deltarpm=0 --enablerepo=remi -y                                                 | 2025-09-04 11:17 | C, E, I, U     |  146 E<
    66 | update --disableplugin=priorities --setopt=deltarpm=0 --enablerepo=remi -y                                                 | 2025-07-03 10:59 | C, E, I, U     |   83 >E
    65 | update --disableplugin=priorities --setopt=deltarpm=0 --enablerepo=remi -y                                                 | 2025-06-18 15:48 | C, E, I, U     |   23  <
    62 | update --disableplugin=priorities --setopt=deltarpm=0 --enablerepo=remi -y                                                 | 2025-05-29 13:25 | C, E, I, U     |  333 ><
    60 | update --disableplugin=priorities --setopt=deltarpm=0 --enablerepo=remi -y                                                 | 2025-05-01 10:41 | C, E, I, U     |   30 ><
    57 | update --disableplugin=priorities --setopt=deltarpm=0 --enablerepo=remi -y                                                 | 2025-04-06 02:28 | C, E, I, U     |   67 ><
     7 | -y update                                                                                                                  | 2025-01-05 02:44 | C, E, I, U     |  246 >E
     6 | -y update                                                                                                                  | 2023-10-26 18:07 | C, E, I, U     |  184 E<
     4 | -y update                                                                                                                  | 2022-12-20 22:37 | I, U           |  198 ><
     1 |                                                                                                                            | 2022-07-27 16:34 | Install        |  311 >E
     
  4. Dec 10, 2025 #4
    eva2000

    eva2000 Administrator Staff Member

    58,893
    12,490
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +19,122
    Local Time:
    2:04 PM
    Nginx 1.31.x
    MariaDB 10.x/11.4+/12.3+
    1. /bin/expr: data: The binary header is destroyed. It should be an executable like my example output, but it is just random data now.
    2. (Bad message): This error corresponds to the Linux error code EBADMSG. It comes directly from the filesystem driver (likely XFS or EXT4) indicating it cannot read the inode or data block due to physical drive failure or logical corruption. This is likely not just a software issue but a storage drive issue. The presence of (Bad message) indicates underlying filesystem corruption (e.g., XFS/EXT4 metadata corruption) or physical disk I/O errors. The binaries are not just "wrong," they are physically unreadable or destroyed on the disk.
    Try reinstalling the affected packages
    Code (Text):
    dnf reinstall coreutils glibc-common -y

    and recheck
    Code (Text):
    file /bin/expr /bin/iconv

    If still doesn't show executable like below, then could be filesystem or drive failure, I'd contact your web host. Who is your web host and how old is the server?
    Code (Text):
    file /bin/expr /bin/iconv
/bin/expr:  ELF 64-bit LSB pie executable, x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, BuildID[sha1]=f096da8553259b5b13e4addb27b061df87bd9f77, for GNU/Linux 3.2.0, stripped
/bin/iconv: ELF 64-bit LSB pie executable, x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, BuildID[sha1]=dd72341337a7f76f6f93f5bb6b85e1ac6a35baaf, for GNU/Linux 3.2.0, stripped
     
  5. Dec 30, 2025 #5
    KlueMaster

    KlueMaster Member

    78
    11
    8
    Aug 5, 2017
    Ratings:
    +32
    Local Time:
    9:34 AM
    MariaDB 10
    I didn't get to check this thread for the last few days. Meanwhile my server was destroyed on a reboot. Thankfully, it was not being used for production. Lessons learned about the webhost, and not using them anymore.

    It was a SSD Nodes server, active since 2020.

    I am now looking for alternative hosts, which can be trusted for data recovery (such snapshots are meaningful instead of same corrupt disk image), and probably early warning for such issues.

    Any opinion on OVHcloud?
     
  6. Dec 30, 2025 #6
    Jon Snow

    Jon Snow Active Member

    917
    188
    43
    Jun 30, 2017
    Ratings:
    +293
    Local Time:
    1:04 AM
    Nginx 1.13.9
    MariaDB 10.1.31
    I only have 1 OVHCloud server in Canada and it works well for me.

    The only issue I ever had with them so far is that I had some connectivity issues when downloading some centminmod files in the past but I downloaded them locally to install centminmod and it's been fine ever since.
     
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