Restore on replicaset "rs1" in state: error: check mongod binary: run: exec: "mongod": executable file not found in $PATH. stderr:

Percona Everest
1

Hi Team,

I’m doing POC for the pbm backup & restore scenarios. I’ve 2 node replicaset and the following is the configuration details,

[root@05d7fd5bde83 ~]# mongo --version
Percona Server for MongoDB shell version v4.4.18-18
Build Info: {
“version”: “4.4.18-18”,
“gitVersion”: “436de76a8593f0207ba7352ca56ee5f5c52b0bb7”,
“openSSLVersion”: “OpenSSL 1.1.1k FIPS 25 Mar 2021”,
“modules”: ,
“allocator”: “tcmalloc”,
“environment”: {
“distarch”: “x86_64”,
“target_arch”: “x86_64”
}
}
[root@05d7fd5bde83 ~]# pbm version
Version: 2.3.0
Platform: linux/amd64
GitCommit: 3b1c2e263901cf041c6b83547f6f28ac2879911f
GitBranch: release-2.3.0
BuildTime: 2023-09-20_14:42_UTC
GoVersion: go1.19
[root@05d7fd5bde83 ~]#

Trying to restore the backup and getting below given error,

[root@mongodb-test6 ~]# pbm restore --time “2024-11-15T09:31:07”
Starting restore 2024-11-15T11:39:38.359619899Z to point-in-time 2024-11-15T09:31:07 from ‘2024-11-14T09:44:16Z’…Error: check mongod binary: run: exec: “mongod”: executable file not found in $PATH. stderr:

  • Restore on replicaset “rs1” in state: error: check mongod binary: run: exec: “mongod”: executable file not found in $PATH. stderr:
    [root@mongodb-test6 ~]#

Kindly assist me on this.

regards,
Jayaprakash Duraisamy

2

And this is the output of pbm status and trying to restore in the same instance.

[root@mongodb-test6 ~]# pbm status
Cluster:

rs1:

  • rs1/192.168.40.116:27017 [S]: pbm-agent v2.3.0 OK
  • rs1/192.168.40.124:27017 [P]: pbm-agent v2.3.0 OK

PITR incremental backup:

Status [ON]

Currently running:

(none)

Backups:

S3 us-west-1 s3://rdscreation-111023-jp/instance3
Snapshots:
2024-11-15T09:37:11Z 6.70MB [restore_to_time: 2024-11-15T09:37:12Z]
2024-11-15T09:31:07Z 16.67MB <incremental, base> [restore_to_time: 2024-11-15T09:31:09Z]
2024-11-15T07:39:41Z 0.00B <incremental, base> [ERROR: upload file /data/db/collection-51--5216000798853528115.wt: get file stat: stat /data/db/collection-51–5216000798853528115.wt: no such file or directory] [2024-11-15T07:39:46Z]
2024-11-14T09:44:16Z 1.49MB [restore_to_time: 2024-11-14T09:44:17Z]
2024-11-14T09:37:51Z 1.45MB <incremental, base> [restore_to_time: 2024-11-14T09:37:53Z]
2024-11-14T09:36:41Z 39.08KB [restore_to_time: 2024-11-14T09:36:46Z]
PITR chunks [47.51MB]:
2024-11-14T09:36:47Z - 2024-11-15T12:09:39Z
2024-11-14T09:09:45Z - 2024-11-14T09:36:46Z (no base snapshot)
2024-11-14T07:09:32Z - 2024-11-14T07:44:13Z (no base snapshot)
[root@mongodb-test6 ~]#

3

Hi Jayaprakash_Duraisam, we hope you are doing great.

I see that you are running pbm 2.4 and psmdb 4.4.

Please Use PBM 2.6 and psmdb 6 for better support from you developers. MongoDB 5.0 was deprecated October 2024 (last month).

Secondly, your error message suggests that PBM could not find PSMDB dependency package which provides mongod binary. Could you please confirm if server mongodb-test6 has mongod binary available? PBM uses that for stopping and stratning mongod processes througout the restore process.

cheers.

4

Hi Arlindo.neto,

Thanks for providing me the updates. Let me try using the pbm 2.6 and psmdb 6 and keep you posted on this.

For the mongod binariy, this is the output,

CONTAINER

[root@05d7fd5bde83 ~]#
[root@05d7fd5bde83 ~]# ls -lrt /usr/bin/mongod
-rwxr-xr-x. 1 root root 71514432 Dec 15 2022 /usr/bin/mongod
[root@05d7fd5bde83 ~]#
[root@05d7fd5bde83 ~]# exit
exit

HOST MACHINE

[root@mongodb-test6 ~]# find / -name mongod
/var/lib/docker/overlay2/944ad8776e1c4e043206b359787ed530eb398fb6bb71a468c9fb4ee06cf13538/diff/etc/sysconfig/mongod
/var/lib/docker/overlay2/944ad8776e1c4e043206b359787ed530eb398fb6bb71a468c9fb4ee06cf13538/diff/usr/bin/mongod
/var/lib/docker/overlay2/944ad8776e1c4e043206b359787ed530eb398fb6bb71a468c9fb4ee06cf13538/diff/var/lib/selinux/targeted/tmp/modules/400/mongod
/var/lib/docker/overlay2/60e23e41c63f2c78dd70a289682920173bf7a8d8677f000557625c608b37ce54/merged/etc/sysconfig/mongod
/var/lib/docker/overlay2/60e23e41c63f2c78dd70a289682920173bf7a8d8677f000557625c608b37ce54/merged/usr/bin/mongod
/var/lib/docker/overlay2/60e23e41c63f2c78dd70a289682920173bf7a8d8677f000557625c608b37ce54/merged/var/lib/selinux/targeted/tmp/modules/400/mongod
[root@mongodb-test6 ~]#

5

Hi,

I see that you are running with containers. I also see that you have this pbm status output:

rs1/192.168.40.116:27017 [S]: pbm-agent v2.3.0 OK
rs1/192.168.40.124:27017 [P]: pbm-agent v2.3.0 OK

I do not know how you are hosting these processes, but if you are using containers:
Run pbm agent processes on the same container , or deploy a podman pod:

If you are using docker, you can use docker compose alternatively.

If you are running on VMs or bare metal servers, You’d have to deploy pbm CLI on one of the nodes. This will fix mongod missing package.

hope it helps.

6

Hello @arlindo.neto

Will look into this and keep you posted on this.